Starting phenix.real_space_refine on Sat Mar 7 10:08:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj8_25157/03_2026/7sj8_25157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj8_25157/03_2026/7sj8_25157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sj8_25157/03_2026/7sj8_25157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj8_25157/03_2026/7sj8_25157.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj8_25157/03_2026/7sj8_25157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj8_25157/03_2026/7sj8_25157.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.317 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 282 5.16 5 C 25802 2.51 5 N 7026 2.21 5 O 7910 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3418 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Chain: "C" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3414 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3367 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 409} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.73, per 1000 atoms: 0.24 Number of scatterers: 41056 At special positions: 0 Unit cell: (171.12, 103.04, 210.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 282 16.00 P 30 15.00 Mg 6 11.99 O 7910 8.00 N 7026 7.00 C 25802 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9624 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 36 sheets defined 54.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.679A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 143 through 161 Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.625A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 143 through 161 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 287 through 297 Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.615A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 Processing helix chain 'J' and resid 71 through 81 removed outlier: 4.641A pdb=" N ILE J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 108 Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 114 through 129 Processing helix chain 'J' and resid 143 through 161 Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 205 through 216 Processing helix chain 'J' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN J 301 " --> pdb=" O PRO J 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 298 through 301' Processing helix chain 'J' and resid 306 through 310 Processing helix chain 'J' and resid 324 through 338 Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.625A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 71 through 81 removed outlier: 4.640A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 129 Processing helix chain 'K' and resid 143 through 161 Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 205 through 216 Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.679A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 Processing helix chain 'K' and resid 287 through 297 Processing helix chain 'K' and resid 298 through 301 removed outlier: 3.614A pdb=" N GLN K 301 " --> pdb=" O PRO K 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 298 through 301' Processing helix chain 'K' and resid 306 through 310 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 401 removed outlier: 3.883A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 71 through 81 removed outlier: 4.641A pdb=" N ILE L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 108 Processing helix chain 'L' and resid 110 through 113 Processing helix chain 'L' and resid 114 through 129 Processing helix chain 'L' and resid 143 through 161 Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 205 through 216 Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.678A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 298 through 301 removed outlier: 3.615A pdb=" N GLN L 301 " --> pdb=" O PRO L 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 298 through 301' Processing helix chain 'L' and resid 306 through 310 Processing helix chain 'L' and resid 324 through 338 Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.884A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.121A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.624A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 108 through 127 removed outlier: 3.962A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 159 Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.659A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 Processing helix chain 'F' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 374 through 391 removed outlier: 3.510A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 40 through 46 removed outlier: 4.144A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.962A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.658A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.511A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.850A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 69 through 79 removed outlier: 4.690A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 108 through 127 removed outlier: 3.963A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 159 Processing helix chain 'G' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN G 184 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 Processing helix chain 'G' and resid 221 through 242 removed outlier: 3.660A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU G 240 " --> pdb=" O VAL G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 285 through 293 Processing helix chain 'G' and resid 295 through 299 Processing helix chain 'G' and resid 304 through 308 Processing helix chain 'G' and resid 322 through 337 Processing helix chain 'G' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE G 341 " --> pdb=" O SER G 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 338 through 341' Processing helix chain 'G' and resid 374 through 391 removed outlier: 3.511A pdb=" N PHE G 378 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 400 removed outlier: 3.828A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.961A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 159 Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.659A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU H 240 " --> pdb=" O VAL H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 285 through 293 Processing helix chain 'H' and resid 295 through 299 Processing helix chain 'H' and resid 304 through 308 Processing helix chain 'H' and resid 322 through 337 Processing helix chain 'H' and resid 338 through 341 removed outlier: 3.607A pdb=" N PHE H 341 " --> pdb=" O SER H 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 338 through 341' Processing helix chain 'H' and resid 374 through 391 removed outlier: 3.512A pdb=" N PHE H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 40 through 46 removed outlier: 4.144A pdb=" N LEU I 44 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 69 through 79 removed outlier: 4.691A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 3.962A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 159 Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.659A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU I 240 " --> pdb=" O VAL I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 285 through 293 Processing helix chain 'I' and resid 295 through 299 Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.606A pdb=" N PHE I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 341' Processing helix chain 'I' and resid 374 through 391 removed outlier: 3.511A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.850A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.143A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 69 through 79 removed outlier: 4.690A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.963A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.699A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.660A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.605A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.510A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 3.829A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.849A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 273 Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'C' and resid 269 through 273 Processing sheet with id=AA7, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'E' and resid 269 through 273 Processing sheet with id=AB1, first strand: chain 'J' and resid 92 through 94 Processing sheet with id=AB2, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'J' and resid 269 through 273 Processing sheet with id=AB4, first strand: chain 'K' and resid 92 through 94 Processing sheet with id=AB5, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'K' and resid 269 through 273 Processing sheet with id=AB7, first strand: chain 'L' and resid 92 through 94 Processing sheet with id=AB8, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'L' and resid 269 through 273 Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AD1, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AD4, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.411A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AD7, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.410A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 51 through 54 2226 hydrogen bonds defined for protein. 6354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.38 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13597 1.34 - 1.46: 7156 1.46 - 1.57: 20753 1.57 - 1.69: 48 1.69 - 1.81: 444 Bond restraints: 41998 Sorted by residual: bond pdb=" N ARG F 359 " pdb=" CA ARG F 359 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.28e+01 bond pdb=" N ARG B 359 " pdb=" CA ARG B 359 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.37e+00 bond pdb=" CA PHE A 169 " pdb=" CB PHE A 169 " ideal model delta sigma weight residual 1.531 1.469 0.061 3.12e-02 1.03e+03 3.86e+00 bond pdb=" N ARG H 359 " pdb=" CA ARG H 359 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 bond pdb=" CA PHE C 169 " pdb=" CB PHE C 169 " ideal model delta sigma weight residual 1.531 1.470 0.061 3.12e-02 1.03e+03 3.83e+00 ... (remaining 41993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 56029 1.79 - 3.58: 872 3.58 - 5.36: 96 5.36 - 7.15: 33 7.15 - 8.94: 5 Bond angle restraints: 57035 Sorted by residual: angle pdb=" C PRO H 358 " pdb=" N ARG H 359 " pdb=" CA ARG H 359 " ideal model delta sigma weight residual 121.54 130.48 -8.94 1.91e+00 2.74e-01 2.19e+01 angle pdb=" C PRO D 358 " pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 121.54 130.39 -8.85 1.91e+00 2.74e-01 2.15e+01 angle pdb=" C PRO I 357 " pdb=" N PRO I 358 " pdb=" CA PRO I 358 " ideal model delta sigma weight residual 119.84 125.09 -5.25 1.25e+00 6.40e-01 1.76e+01 angle pdb=" N GLY I 360 " pdb=" CA GLY I 360 " pdb=" C GLY I 360 " ideal model delta sigma weight residual 114.95 109.19 5.76 1.41e+00 5.03e-01 1.67e+01 angle pdb=" N ARG G 359 " pdb=" CA ARG G 359 " pdb=" C ARG G 359 " ideal model delta sigma weight residual 110.80 118.89 -8.09 2.13e+00 2.20e-01 1.44e+01 ... (remaining 57030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 24204 28.64 - 57.28: 651 57.28 - 85.92: 66 85.92 - 114.56: 12 114.56 - 143.20: 12 Dihedral angle restraints: 24945 sinusoidal: 9957 harmonic: 14988 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -147.53 -143.20 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -147.55 -143.19 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -147.55 -143.18 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 24942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5373 0.065 - 0.129: 846 0.129 - 0.194: 16 0.194 - 0.258: 0 0.258 - 0.323: 5 Chirality restraints: 6240 Sorted by residual: chirality pdb=" CA ARG I 359 " pdb=" N ARG I 359 " pdb=" C ARG I 359 " pdb=" CB ARG I 359 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ARG B 359 " pdb=" N ARG B 359 " pdb=" C ARG B 359 " pdb=" CB ARG B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA ARG H 359 " pdb=" N ARG H 359 " pdb=" C ARG H 359 " pdb=" CB ARG H 359 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 6237 not shown) Planarity restraints: 7411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 380 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ARG B 380 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG B 380 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE B 381 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 358 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C PRO H 358 " -0.025 2.00e-02 2.50e+03 pdb=" O PRO H 358 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG H 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 380 " -0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C ARG F 380 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG F 380 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE F 381 " -0.008 2.00e-02 2.50e+03 ... (remaining 7408 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 511 2.51 - 3.10: 33177 3.10 - 3.70: 65739 3.70 - 4.30: 90910 4.30 - 4.90: 154739 Nonbonded interactions: 345076 Sorted by model distance: nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.906 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.907 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.907 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.907 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.907 2.170 ... (remaining 345071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 253 or (resid 254 and (name N or name CA or name \ C or name O or name CB )) or resid 255 through 502)) selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 39.340 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 41998 Z= 0.251 Angle : 0.600 8.939 57035 Z= 0.337 Chirality : 0.043 0.323 6240 Planarity : 0.004 0.035 7411 Dihedral : 13.420 143.203 15321 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.46 % Favored : 95.44 % Rotamer: Outliers : 6.00 % Allowed : 6.77 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.12), residues: 5136 helix: 0.47 (0.10), residues: 2442 sheet: -1.24 (0.19), residues: 738 loop : -1.85 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 156 TYR 0.010 0.001 TYR D 36 PHE 0.011 0.001 PHE F 367 TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS D 264 Details of bonding type rmsd covalent geometry : bond 0.00516 (41998) covalent geometry : angle 0.59958 (57035) hydrogen bonds : bond 0.15876 ( 2184) hydrogen bonds : angle 6.78430 ( 6354) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2374 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 265 poor density : 2109 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 GLU cc_start: 0.7610 (mp0) cc_final: 0.6831 (mm-30) REVERT: A 6 SER cc_start: 0.9179 (m) cc_final: 0.8801 (p) REVERT: A 33 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8155 (p0) REVERT: A 77 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8919 (tp30) REVERT: A 90 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7783 (tm-30) REVERT: A 103 TYR cc_start: 0.8942 (t80) cc_final: 0.8527 (t80) REVERT: A 120 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8054 (t70) REVERT: A 121 ARG cc_start: 0.8261 (mmm160) cc_final: 0.7863 (tpt170) REVERT: A 209 ILE cc_start: 0.9121 (mt) cc_final: 0.8857 (mm) REVERT: A 224 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7528 (m-10) REVERT: A 423 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8443 (mt-10) REVERT: A 430 LYS cc_start: 0.9434 (ttmt) cc_final: 0.9185 (tptt) REVERT: C 1 MET cc_start: 0.7549 (ptp) cc_final: 0.7114 (ptp) REVERT: C 6 SER cc_start: 0.9123 (m) cc_final: 0.8772 (p) REVERT: C 11 GLN cc_start: 0.8380 (tt0) cc_final: 0.8119 (tt0) REVERT: C 60 LYS cc_start: 0.8677 (tttp) cc_final: 0.8046 (tttt) REVERT: C 101 ASN cc_start: 0.9204 (m-40) cc_final: 0.8869 (m-40) REVERT: C 269 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8239 (pp) REVERT: C 282 TYR cc_start: 0.8476 (m-80) cc_final: 0.8017 (m-80) REVERT: C 358 GLN cc_start: 0.9284 (tp40) cc_final: 0.8980 (tp40) REVERT: C 414 GLU cc_start: 0.7630 (tt0) cc_final: 0.7408 (mt-10) REVERT: E 1 MET cc_start: 0.7555 (ptp) cc_final: 0.7070 (ptp) REVERT: E 3 GLU cc_start: 0.7752 (mp0) cc_final: 0.6503 (mm-30) REVERT: E 6 SER cc_start: 0.9186 (m) cc_final: 0.8776 (p) REVERT: E 18 ASN cc_start: 0.9031 (m-40) cc_final: 0.8752 (m110) REVERT: E 33 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8364 (p0) REVERT: E 55 GLU cc_start: 0.8559 (tt0) cc_final: 0.8188 (tp30) REVERT: E 90 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7694 (tm-30) REVERT: E 129 CYS cc_start: 0.7103 (m) cc_final: 0.6899 (m) REVERT: E 154 MET cc_start: 0.8895 (mmm) cc_final: 0.8666 (mmm) REVERT: E 156 ARG cc_start: 0.8909 (mmt90) cc_final: 0.8622 (mmm-85) REVERT: E 167 LEU cc_start: 0.9498 (mt) cc_final: 0.9079 (mt) REVERT: E 169 PHE cc_start: 0.8790 (m-80) cc_final: 0.8356 (m-80) REVERT: E 209 ILE cc_start: 0.9280 (mt) cc_final: 0.8926 (mt) REVERT: E 220 GLU cc_start: 0.7363 (mp0) cc_final: 0.7099 (mp0) REVERT: E 309 HIS cc_start: 0.8256 (m170) cc_final: 0.8047 (m90) REVERT: E 358 GLN cc_start: 0.9363 (tp40) cc_final: 0.9141 (tp40) REVERT: E 382 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8715 (p) REVERT: E 386 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: E 423 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8479 (mt-10) REVERT: E 430 LYS cc_start: 0.9600 (ttmt) cc_final: 0.9338 (tptt) REVERT: J 3 GLU cc_start: 0.7521 (mp0) cc_final: 0.6116 (mm-30) REVERT: J 33 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.7953 (p0) REVERT: J 69 ASP cc_start: 0.7948 (t0) cc_final: 0.7651 (t0) REVERT: J 75 ILE cc_start: 0.9407 (mm) cc_final: 0.9157 (mt) REVERT: J 90 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7781 (tp30) REVERT: J 129 CYS cc_start: 0.6887 (m) cc_final: 0.5330 (m) REVERT: J 198 SER cc_start: 0.7668 (p) cc_final: 0.7152 (p) REVERT: J 220 GLU cc_start: 0.7724 (mp0) cc_final: 0.7448 (mp0) REVERT: J 244 PHE cc_start: 0.8669 (m-80) cc_final: 0.8173 (m-80) REVERT: J 280 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8027 (mtmm) REVERT: J 291 ILE cc_start: 0.9387 (pt) cc_final: 0.8625 (pt) REVERT: J 295 CYS cc_start: 0.8682 (m) cc_final: 0.8398 (m) REVERT: J 296 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7910 (t80) REVERT: J 302 MET cc_start: 0.7818 (mtt) cc_final: 0.7608 (mtt) REVERT: J 316 CYS cc_start: 0.8485 (t) cc_final: 0.8113 (t) REVERT: J 346 TRP cc_start: 0.8291 (p-90) cc_final: 0.4960 (t-100) REVERT: J 430 LYS cc_start: 0.9591 (ttmt) cc_final: 0.9336 (tptt) REVERT: K 24 TYR cc_start: 0.8799 (m-10) cc_final: 0.8503 (m-80) REVERT: K 33 ASP cc_start: 0.8732 (OUTLIER) cc_final: 0.7887 (p0) REVERT: K 88 HIS cc_start: 0.8504 (t70) cc_final: 0.8221 (t70) REVERT: K 90 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7664 (tp30) REVERT: K 103 TYR cc_start: 0.8587 (t80) cc_final: 0.8236 (t80) REVERT: K 198 SER cc_start: 0.7848 (p) cc_final: 0.6955 (p) REVERT: K 256 GLN cc_start: 0.9019 (pt0) cc_final: 0.8639 (tm-30) REVERT: K 295 CYS cc_start: 0.8688 (m) cc_final: 0.8479 (m) REVERT: K 296 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7988 (t80) REVERT: K 311 LYS cc_start: 0.8564 (mttm) cc_final: 0.8164 (mtpp) REVERT: K 346 TRP cc_start: 0.8583 (p-90) cc_final: 0.4752 (t-100) REVERT: K 430 LYS cc_start: 0.9456 (ttmt) cc_final: 0.9208 (tptt) REVERT: K 433 GLU cc_start: 0.9121 (tt0) cc_final: 0.8898 (tp30) REVERT: L 11 GLN cc_start: 0.8107 (tt0) cc_final: 0.7781 (tt0) REVERT: L 69 ASP cc_start: 0.7718 (t0) cc_final: 0.7501 (t0) REVERT: L 88 HIS cc_start: 0.8747 (t70) cc_final: 0.8113 (t70) REVERT: L 90 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8038 (tp30) REVERT: L 198 SER cc_start: 0.7868 (p) cc_final: 0.7431 (p) REVERT: L 224 TYR cc_start: 0.8428 (OUTLIER) cc_final: 0.7879 (m-10) REVERT: L 244 PHE cc_start: 0.8873 (m-80) cc_final: 0.8322 (m-80) REVERT: L 257 THR cc_start: 0.9003 (m) cc_final: 0.8795 (p) REVERT: L 295 CYS cc_start: 0.8681 (m) cc_final: 0.8447 (m) REVERT: L 311 LYS cc_start: 0.8536 (mttm) cc_final: 0.7995 (mtpp) REVERT: L 346 TRP cc_start: 0.8416 (p-90) cc_final: 0.4978 (t-100) REVERT: L 417 GLU cc_start: 0.8749 (tt0) cc_final: 0.8441 (mt-10) REVERT: F 2 ARG cc_start: 0.8298 (mtm180) cc_final: 0.8003 (mtm180) REVERT: F 19 LYS cc_start: 0.8453 (tptt) cc_final: 0.7913 (mmmt) REVERT: F 20 PHE cc_start: 0.8864 (t80) cc_final: 0.8654 (t80) REVERT: F 22 GLU cc_start: 0.7829 (tt0) cc_final: 0.7024 (tt0) REVERT: F 50 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: F 99 ASN cc_start: 0.8178 (t0) cc_final: 0.7939 (t0) REVERT: F 106 TYR cc_start: 0.8004 (m-80) cc_final: 0.7694 (m-10) REVERT: F 134 GLN cc_start: 0.8245 (pt0) cc_final: 0.7972 (pt0) REVERT: F 159 TYR cc_start: 0.8631 (m-80) cc_final: 0.8207 (m-80) REVERT: F 226 ASN cc_start: 0.9058 (m-40) cc_final: 0.8804 (m-40) REVERT: F 251 ARG cc_start: 0.8632 (tpp80) cc_final: 0.8394 (mtp85) REVERT: F 364 SER cc_start: 0.8790 (p) cc_final: 0.8535 (m) REVERT: F 401 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7646 (mm-30) REVERT: F 406 MET cc_start: 0.8496 (tpp) cc_final: 0.8292 (tpp) REVERT: D 8 GLN cc_start: 0.8055 (mt0) cc_final: 0.7687 (mt0) REVERT: D 26 ASP cc_start: 0.8377 (m-30) cc_final: 0.7128 (m-30) REVERT: D 99 ASN cc_start: 0.8314 (t0) cc_final: 0.7972 (t0) REVERT: D 123 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8257 (mm-30) REVERT: D 279 GLN cc_start: 0.8609 (pt0) cc_final: 0.8145 (pt0) REVERT: D 306 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8552 (mtm110) REVERT: D 310 TYR cc_start: 0.8857 (m-80) cc_final: 0.8605 (m-80) REVERT: D 329 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8333 (mm-40) REVERT: G 6 HIS cc_start: 0.8687 (t70) cc_final: 0.8245 (t70) REVERT: G 8 GLN cc_start: 0.8497 (mt0) cc_final: 0.7955 (mt0) REVERT: G 14 ASN cc_start: 0.8980 (m-40) cc_final: 0.8751 (m-40) REVERT: G 27 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8461 (mt-10) REVERT: G 31 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8243 (t70) REVERT: G 67 ASP cc_start: 0.8566 (t0) cc_final: 0.8072 (t0) REVERT: G 69 GLU cc_start: 0.8089 (pt0) cc_final: 0.7780 (mp0) REVERT: G 108 GLU cc_start: 0.9088 (tp30) cc_final: 0.8547 (tp30) REVERT: G 121 ARG cc_start: 0.8788 (ttm110) cc_final: 0.8016 (mtm180) REVERT: G 123 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9316 (tp30) REVERT: G 129 CYS cc_start: 0.7674 (t) cc_final: 0.7318 (t) REVERT: G 136 THR cc_start: 0.8813 (m) cc_final: 0.8389 (p) REVERT: G 143 THR cc_start: 0.8618 (m) cc_final: 0.8413 (m) REVERT: G 164 MET cc_start: 0.8861 (tpp) cc_final: 0.8623 (mtm) REVERT: G 184 ASN cc_start: 0.9066 (m-40) cc_final: 0.8513 (p0) REVERT: G 194 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8629 (mt-10) REVERT: G 197 ASP cc_start: 0.8046 (m-30) cc_final: 0.7807 (m-30) REVERT: G 207 LEU cc_start: 0.9447 (mp) cc_final: 0.9087 (mp) REVERT: G 209 ASP cc_start: 0.8667 (t0) cc_final: 0.8281 (t70) REVERT: G 211 CYS cc_start: 0.8916 (m) cc_final: 0.8699 (m) REVERT: G 213 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7164 (ttp-110) REVERT: G 288 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8013 (tm-30) REVERT: G 304 ASP cc_start: 0.8472 (t0) cc_final: 0.8264 (t70) REVERT: G 306 ARG cc_start: 0.9087 (mtt90) cc_final: 0.8805 (mtm110) REVERT: G 379 LYS cc_start: 0.9418 (mtpt) cc_final: 0.8967 (mtmm) REVERT: G 395 LEU cc_start: 0.9375 (tp) cc_final: 0.9128 (tp) REVERT: G 401 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7933 (mm-30) REVERT: G 404 ASP cc_start: 0.8135 (p0) cc_final: 0.7510 (p0) REVERT: H 20 PHE cc_start: 0.9325 (t80) cc_final: 0.9068 (t80) REVERT: H 27 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8196 (mt-10) REVERT: H 31 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8022 (t70) REVERT: H 50 TYR cc_start: 0.8073 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: H 67 ASP cc_start: 0.8409 (t0) cc_final: 0.8146 (t0) REVERT: H 68 LEU cc_start: 0.8320 (mt) cc_final: 0.8113 (mp) REVERT: H 108 GLU cc_start: 0.8758 (tp30) cc_final: 0.8546 (tp30) REVERT: H 121 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8159 (mtm180) REVERT: H 130 LEU cc_start: 0.8802 (tp) cc_final: 0.8548 (tp) REVERT: H 181 GLU cc_start: 0.8572 (pt0) cc_final: 0.8325 (pt0) REVERT: H 184 ASN cc_start: 0.8968 (m-40) cc_final: 0.8456 (p0) REVERT: H 194 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8522 (mt-10) REVERT: H 207 LEU cc_start: 0.9438 (mp) cc_final: 0.9233 (mp) REVERT: H 209 ASP cc_start: 0.8689 (t0) cc_final: 0.8112 (t0) REVERT: H 252 LYS cc_start: 0.8806 (mtpt) cc_final: 0.8439 (mtpp) REVERT: H 304 ASP cc_start: 0.8428 (t0) cc_final: 0.8111 (t70) REVERT: H 395 LEU cc_start: 0.9326 (tp) cc_final: 0.9087 (tp) REVERT: H 404 ASP cc_start: 0.8492 (p0) cc_final: 0.7845 (p0) REVERT: H 407 GLU cc_start: 0.9078 (tp30) cc_final: 0.8826 (mm-30) REVERT: H 410 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8940 (mt-10) REVERT: I 31 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8272 (t70) REVERT: I 67 ASP cc_start: 0.8558 (t0) cc_final: 0.8255 (t0) REVERT: I 88 ASP cc_start: 0.7707 (p0) cc_final: 0.7267 (p0) REVERT: I 108 GLU cc_start: 0.8937 (tp30) cc_final: 0.8615 (tp30) REVERT: I 121 ARG cc_start: 0.8750 (ttm110) cc_final: 0.8082 (mtm180) REVERT: I 123 GLU cc_start: 0.9436 (mm-30) cc_final: 0.9014 (mm-30) REVERT: I 129 CYS cc_start: 0.7738 (t) cc_final: 0.7504 (t) REVERT: I 181 GLU cc_start: 0.8842 (pt0) cc_final: 0.8605 (pt0) REVERT: I 184 ASN cc_start: 0.9004 (m-40) cc_final: 0.8420 (p0) REVERT: I 209 ASP cc_start: 0.8786 (t0) cc_final: 0.8353 (t0) REVERT: I 240 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8814 (pt) REVERT: I 252 LYS cc_start: 0.8990 (mtpt) cc_final: 0.8562 (mttp) REVERT: I 343 GLU cc_start: 0.8735 (tp30) cc_final: 0.8532 (tp30) REVERT: I 376 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8553 (mt-10) REVERT: I 395 LEU cc_start: 0.9375 (tp) cc_final: 0.9174 (tp) REVERT: I 401 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8108 (mm-30) REVERT: I 404 ASP cc_start: 0.8396 (p0) cc_final: 0.7639 (p0) REVERT: I 407 GLU cc_start: 0.9241 (tp30) cc_final: 0.9015 (mm-30) REVERT: B 26 ASP cc_start: 0.8410 (m-30) cc_final: 0.7195 (m-30) REVERT: B 27 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 159 TYR cc_start: 0.8335 (m-80) cc_final: 0.7707 (m-80) REVERT: B 289 LEU cc_start: 0.9170 (mp) cc_final: 0.8951 (mt) REVERT: B 316 VAL cc_start: 0.9381 (t) cc_final: 0.9158 (m) REVERT: B 329 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8230 (mm110) REVERT: B 412 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 424 GLN cc_start: 0.8384 (tt0) cc_final: 0.8116 (tt0) outliers start: 265 outliers final: 119 residues processed: 2281 average time/residue: 0.2389 time to fit residues: 878.6132 Evaluate side-chains 1625 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1488 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 216 ASN Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 296 PHE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 382 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 216 ASN Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 420 GLU Chi-restraints excluded: chain K residue 33 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 386 GLU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 216 ASN Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 339 ARG Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 290 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 290 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 290 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 122 LYS Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 290 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 290 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0670 chunk 494 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 283 HIS ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 256 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN E 256 GLN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN J 101 ASN J 128 GLN J 206 ASN ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS K 11 GLN ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 35 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 423 GLN F 426 GLN D 11 GLN D 298 ASN D 307 HIS D 423 GLN D 426 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 337 ASN H 165 ASN H 227 HIS H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS B 99 ASN B 165 ASN B 298 ASN B 307 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.108523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.092175 restraints weight = 88256.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.095368 restraints weight = 44206.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.097606 restraints weight = 26537.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099169 restraints weight = 18178.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.100260 restraints weight = 13576.298| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41998 Z= 0.188 Angle : 0.653 10.948 57035 Z= 0.339 Chirality : 0.046 0.212 6240 Planarity : 0.005 0.070 7411 Dihedral : 11.049 137.636 5997 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % Rotamer: Outliers : 5.98 % Allowed : 17.77 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.12), residues: 5136 helix: 1.09 (0.10), residues: 2496 sheet: -1.17 (0.18), residues: 804 loop : -1.75 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 390 TYR 0.021 0.001 TYR C 210 PHE 0.025 0.002 PHE L 255 TRP 0.014 0.001 TRP D 21 HIS 0.024 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00411 (41998) covalent geometry : angle 0.65300 (57035) hydrogen bonds : bond 0.05353 ( 2184) hydrogen bonds : angle 5.34969 ( 6354) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1977 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 1713 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASN cc_start: 0.9132 (m110) cc_final: 0.8913 (m110) REVERT: A 71 GLU cc_start: 0.7320 (pt0) cc_final: 0.6915 (pt0) REVERT: A 90 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7747 (tm-30) REVERT: A 96 LYS cc_start: 0.8794 (tppt) cc_final: 0.8557 (tppp) REVERT: A 103 TYR cc_start: 0.8854 (t80) cc_final: 0.8372 (t80) REVERT: A 120 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7963 (t70) REVERT: A 121 ARG cc_start: 0.8235 (mmm160) cc_final: 0.7804 (tpt170) REVERT: A 149 PHE cc_start: 0.8827 (t80) cc_final: 0.8595 (t80) REVERT: A 169 PHE cc_start: 0.8566 (m-80) cc_final: 0.8322 (m-80) REVERT: A 196 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7910 (tm-30) REVERT: A 211 ASP cc_start: 0.8903 (t0) cc_final: 0.8430 (t70) REVERT: A 302 MET cc_start: 0.8301 (mtt) cc_final: 0.8055 (mtm) REVERT: A 309 HIS cc_start: 0.8072 (m90) cc_final: 0.7869 (m90) REVERT: A 327 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8539 (p0) REVERT: A 357 TYR cc_start: 0.8630 (m-80) cc_final: 0.8198 (m-80) REVERT: A 372 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7154 (mm-40) REVERT: A 430 LYS cc_start: 0.9380 (ttmt) cc_final: 0.9078 (tptt) REVERT: C 66 VAL cc_start: 0.9230 (t) cc_final: 0.8988 (p) REVERT: C 96 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8480 (tppp) REVERT: C 156 ARG cc_start: 0.8744 (mmt90) cc_final: 0.8345 (mmm-85) REVERT: C 238 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8603 (mt) REVERT: C 269 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8177 (pp) REVERT: C 358 GLN cc_start: 0.9300 (tp40) cc_final: 0.8924 (tp40) REVERT: E 3 GLU cc_start: 0.7606 (mp0) cc_final: 0.6709 (mm-30) REVERT: E 6 SER cc_start: 0.9134 (m) cc_final: 0.8728 (p) REVERT: E 50 ASN cc_start: 0.8302 (p0) cc_final: 0.8041 (p0) REVERT: E 90 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7671 (tm-30) REVERT: E 156 ARG cc_start: 0.8941 (mmt90) cc_final: 0.8649 (mmm-85) REVERT: E 196 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8177 (tm-30) REVERT: E 255 PHE cc_start: 0.8399 (m-80) cc_final: 0.8137 (m-80) REVERT: E 256 GLN cc_start: 0.9508 (pt0) cc_final: 0.9294 (pt0) REVERT: E 351 PHE cc_start: 0.7998 (m-80) cc_final: 0.7777 (m-80) REVERT: E 352 LYS cc_start: 0.8608 (tttp) cc_final: 0.7781 (ttmp) REVERT: E 386 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.6822 (tm-30) REVERT: E 422 ARG cc_start: 0.8807 (tpt90) cc_final: 0.8405 (tpt-90) REVERT: E 423 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8484 (mt-10) REVERT: E 430 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9241 (tptt) REVERT: J 69 ASP cc_start: 0.8350 (t0) cc_final: 0.8083 (t0) REVERT: J 75 ILE cc_start: 0.9379 (mm) cc_final: 0.9029 (mt) REVERT: J 76 ASP cc_start: 0.8842 (m-30) cc_final: 0.8598 (m-30) REVERT: J 214 ARG cc_start: 0.8952 (tmm-80) cc_final: 0.8239 (ttp80) REVERT: J 244 PHE cc_start: 0.8782 (m-80) cc_final: 0.8210 (m-80) REVERT: J 258 ASN cc_start: 0.9285 (m-40) cc_final: 0.9059 (m110) REVERT: J 296 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7573 (t80) REVERT: J 308 ARG cc_start: 0.8944 (mpp80) cc_final: 0.8213 (ptp90) REVERT: J 316 CYS cc_start: 0.8804 (t) cc_final: 0.8457 (t) REVERT: J 341 ILE cc_start: 0.8230 (mp) cc_final: 0.7545 (mp) REVERT: J 346 TRP cc_start: 0.8418 (p-90) cc_final: 0.4829 (t-100) REVERT: J 430 LYS cc_start: 0.9584 (ttmt) cc_final: 0.9290 (tptt) REVERT: J 432 TYR cc_start: 0.8647 (m-80) cc_final: 0.7717 (t80) REVERT: K 76 ASP cc_start: 0.8751 (m-30) cc_final: 0.8472 (m-30) REVERT: K 90 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7756 (tp30) REVERT: K 96 LYS cc_start: 0.8959 (tppt) cc_final: 0.8750 (mmmt) REVERT: K 198 SER cc_start: 0.7987 (p) cc_final: 0.7681 (p) REVERT: K 203 MET cc_start: 0.9082 (mmt) cc_final: 0.8737 (mmp) REVERT: K 256 GLN cc_start: 0.9035 (pt0) cc_final: 0.8644 (tm-30) REVERT: K 327 ASP cc_start: 0.9283 (OUTLIER) cc_final: 0.8735 (p0) REVERT: K 346 TRP cc_start: 0.8618 (p-90) cc_final: 0.4533 (t-100) REVERT: K 357 TYR cc_start: 0.8558 (m-80) cc_final: 0.8110 (m-80) REVERT: K 430 LYS cc_start: 0.9519 (ttmt) cc_final: 0.9192 (tptt) REVERT: K 433 GLU cc_start: 0.9212 (tt0) cc_final: 0.8880 (tp30) REVERT: L 69 ASP cc_start: 0.8271 (t0) cc_final: 0.7925 (t70) REVERT: L 76 ASP cc_start: 0.8850 (m-30) cc_final: 0.8413 (m-30) REVERT: L 90 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8132 (tp30) REVERT: L 224 TYR cc_start: 0.8272 (OUTLIER) cc_final: 0.7819 (m-10) REVERT: L 255 PHE cc_start: 0.8874 (m-80) cc_final: 0.8635 (m-80) REVERT: L 258 ASN cc_start: 0.9359 (m-40) cc_final: 0.9110 (m-40) REVERT: L 297 GLU cc_start: 0.9160 (tp30) cc_final: 0.8896 (tp30) REVERT: L 304 LYS cc_start: 0.9469 (tppp) cc_final: 0.9226 (tppp) REVERT: L 346 TRP cc_start: 0.8361 (p-90) cc_final: 0.4763 (t-100) REVERT: L 351 PHE cc_start: 0.8095 (m-80) cc_final: 0.7840 (m-80) REVERT: L 352 LYS cc_start: 0.2761 (mmtt) cc_final: 0.2204 (tppt) REVERT: L 394 LYS cc_start: 0.8869 (mppt) cc_final: 0.8562 (mppt) REVERT: F 2 ARG cc_start: 0.8411 (mtm180) cc_final: 0.8137 (mtm180) REVERT: F 14 ASN cc_start: 0.8865 (m-40) cc_final: 0.8571 (m-40) REVERT: F 22 GLU cc_start: 0.8576 (tt0) cc_final: 0.8219 (tm-30) REVERT: F 45 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8463 (mt-10) REVERT: F 134 GLN cc_start: 0.8876 (pt0) cc_final: 0.8560 (pt0) REVERT: F 164 MET cc_start: 0.9069 (tpp) cc_final: 0.8822 (tpp) REVERT: F 251 ARG cc_start: 0.9082 (tpp80) cc_final: 0.8814 (mtp85) REVERT: F 290 THR cc_start: 0.9665 (m) cc_final: 0.9438 (p) REVERT: F 329 GLN cc_start: 0.9264 (tp40) cc_final: 0.9032 (mm110) REVERT: F 375 GLN cc_start: 0.8401 (pp30) cc_final: 0.6945 (pp30) REVERT: F 379 LYS cc_start: 0.9537 (ttpp) cc_final: 0.9328 (mtmt) REVERT: F 405 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8060 (tm-30) REVERT: F 406 MET cc_start: 0.8631 (tpp) cc_final: 0.8097 (tpp) REVERT: D 6 HIS cc_start: 0.8765 (t-170) cc_final: 0.8354 (t-170) REVERT: D 8 GLN cc_start: 0.8363 (mt0) cc_final: 0.8031 (mt0) REVERT: D 22 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 26 ASP cc_start: 0.8445 (m-30) cc_final: 0.7987 (m-30) REVERT: D 99 ASN cc_start: 0.8308 (t0) cc_final: 0.8028 (t0) REVERT: D 108 GLU cc_start: 0.8628 (tp30) cc_final: 0.8391 (tp30) REVERT: D 122 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9108 (tptt) REVERT: D 194 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8438 (mm-30) REVERT: D 209 ASP cc_start: 0.8703 (t0) cc_final: 0.7875 (t0) REVERT: D 279 GLN cc_start: 0.8647 (pt0) cc_final: 0.8177 (pt0) REVERT: D 289 LEU cc_start: 0.9361 (mp) cc_final: 0.9145 (mt) REVERT: D 310 TYR cc_start: 0.9163 (m-80) cc_final: 0.8933 (m-80) REVERT: D 323 MET cc_start: 0.8306 (mpp) cc_final: 0.7641 (mpp) REVERT: D 325 GLU cc_start: 0.8719 (tt0) cc_final: 0.8350 (pt0) REVERT: D 364 SER cc_start: 0.8858 (p) cc_final: 0.8594 (p) REVERT: D 375 GLN cc_start: 0.8671 (pp30) cc_final: 0.7269 (pp30) REVERT: D 379 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8452 (mtmt) REVERT: D 405 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8124 (tm-30) REVERT: G 8 GLN cc_start: 0.8622 (mt0) cc_final: 0.8239 (mt0) REVERT: G 14 ASN cc_start: 0.8983 (m-40) cc_final: 0.8711 (m-40) REVERT: G 31 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8539 (m-30) REVERT: G 50 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: G 121 ARG cc_start: 0.8789 (ttm110) cc_final: 0.8331 (mtm180) REVERT: G 123 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9175 (tp30) REVERT: G 143 THR cc_start: 0.8702 (m) cc_final: 0.8420 (m) REVERT: G 194 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8811 (mt-10) REVERT: G 197 ASP cc_start: 0.8150 (m-30) cc_final: 0.7844 (m-30) REVERT: G 207 LEU cc_start: 0.9459 (mp) cc_final: 0.9117 (mp) REVERT: G 209 ASP cc_start: 0.8673 (t0) cc_final: 0.8393 (t0) REVERT: G 211 CYS cc_start: 0.8908 (m) cc_final: 0.8688 (m) REVERT: G 213 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7613 (ttp-110) REVERT: G 226 ASN cc_start: 0.9003 (m-40) cc_final: 0.8730 (m-40) REVERT: G 237 THR cc_start: 0.8952 (m) cc_final: 0.8066 (t) REVERT: G 306 ARG cc_start: 0.9145 (mtt90) cc_final: 0.8763 (mtm110) REVERT: G 325 GLU cc_start: 0.8903 (tt0) cc_final: 0.8209 (tt0) REVERT: G 370 ASN cc_start: 0.8595 (t0) cc_final: 0.8375 (t0) REVERT: G 375 GLN cc_start: 0.8096 (pp30) cc_final: 0.7632 (pp30) REVERT: G 401 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7962 (mm-30) REVERT: H 20 PHE cc_start: 0.9183 (t80) cc_final: 0.8947 (t80) REVERT: H 31 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: H 46 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8372 (mmm-85) REVERT: H 50 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: H 121 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8263 (mtm180) REVERT: H 195 ASN cc_start: 0.9063 (m-40) cc_final: 0.8848 (m-40) REVERT: H 209 ASP cc_start: 0.8766 (t0) cc_final: 0.8561 (t0) REVERT: H 323 MET cc_start: 0.8440 (mmm) cc_final: 0.7835 (mpp) REVERT: H 325 GLU cc_start: 0.8679 (tt0) cc_final: 0.8378 (tt0) REVERT: H 370 ASN cc_start: 0.8435 (t0) cc_final: 0.8079 (t0) REVERT: H 379 LYS cc_start: 0.9449 (ttmt) cc_final: 0.8901 (mtmm) REVERT: H 392 LYS cc_start: 0.9054 (mtmt) cc_final: 0.8632 (mtpt) REVERT: I 69 GLU cc_start: 0.8060 (mp0) cc_final: 0.7517 (mp0) REVERT: I 77 ARG cc_start: 0.9262 (ttm170) cc_final: 0.8966 (ttm110) REVERT: I 108 GLU cc_start: 0.8700 (tp30) cc_final: 0.8491 (tp30) REVERT: I 121 ARG cc_start: 0.8746 (ttm110) cc_final: 0.8293 (mtm180) REVERT: I 123 GLU cc_start: 0.9432 (mm-30) cc_final: 0.8942 (mm-30) REVERT: I 383 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8444 (tm-30) REVERT: I 398 TYR cc_start: 0.9193 (m-80) cc_final: 0.8988 (m-10) REVERT: I 405 GLU cc_start: 0.7882 (pp20) cc_final: 0.7304 (tm-30) REVERT: B 6 HIS cc_start: 0.8544 (t-170) cc_final: 0.8284 (t-170) REVERT: B 57 HIS cc_start: 0.6574 (t-170) cc_final: 0.6129 (t70) REVERT: B 59 TYR cc_start: 0.7999 (m-80) cc_final: 0.7740 (m-80) REVERT: B 73 MET cc_start: 0.8856 (mmm) cc_final: 0.8566 (mtt) REVERT: B 99 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8229 (t0) REVERT: B 108 GLU cc_start: 0.8513 (tp30) cc_final: 0.8296 (tp30) REVERT: B 159 TYR cc_start: 0.8384 (m-80) cc_final: 0.7981 (m-80) REVERT: B 288 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8161 (mt-10) REVERT: B 329 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8680 (mm110) REVERT: B 405 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7884 (tm-30) REVERT: B 424 GLN cc_start: 0.8696 (tt0) cc_final: 0.8285 (tt0) outliers start: 264 outliers final: 161 residues processed: 1853 average time/residue: 0.2299 time to fit residues: 697.1357 Evaluate side-chains 1669 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1494 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 296 PHE Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 377 MET Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 379 SER Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 413 MET Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 322 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 452 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 361 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 272 optimal weight: 0.9980 chunk 392 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 480 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN C 285 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN K 128 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS F 423 GLN F 424 GLN D 298 ASN D 307 HIS D 337 ASN D 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN B 298 ASN B 307 HIS B 423 GLN B 426 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.090471 restraints weight = 89537.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093710 restraints weight = 44341.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.095892 restraints weight = 27038.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097427 restraints weight = 18716.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.098515 restraints weight = 14092.511| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 41998 Z= 0.214 Angle : 0.655 14.877 57035 Z= 0.340 Chirality : 0.046 0.245 6240 Planarity : 0.005 0.046 7411 Dihedral : 10.727 137.865 5923 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 7.09 % Allowed : 20.24 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.12), residues: 5136 helix: 1.12 (0.10), residues: 2472 sheet: -1.21 (0.19), residues: 786 loop : -1.73 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 339 TYR 0.038 0.002 TYR C 210 PHE 0.022 0.002 PHE J 255 TRP 0.011 0.001 TRP E 21 HIS 0.007 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00467 (41998) covalent geometry : angle 0.65495 (57035) hydrogen bonds : bond 0.05043 ( 2184) hydrogen bonds : angle 5.16536 ( 6354) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1836 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 313 poor density : 1523 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.7226 (pt0) cc_final: 0.6718 (pt0) REVERT: A 90 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7760 (tm-30) REVERT: A 96 LYS cc_start: 0.8819 (tppt) cc_final: 0.8416 (tppp) REVERT: A 103 TYR cc_start: 0.8827 (t80) cc_final: 0.8506 (t80) REVERT: A 120 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8071 (t70) REVERT: A 121 ARG cc_start: 0.8299 (mmm160) cc_final: 0.7888 (tpt170) REVERT: A 169 PHE cc_start: 0.8589 (m-80) cc_final: 0.8272 (m-80) REVERT: A 254 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (mp0) REVERT: A 306 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7635 (p0) REVERT: A 309 HIS cc_start: 0.8019 (m90) cc_final: 0.7789 (m90) REVERT: A 327 ASP cc_start: 0.9084 (OUTLIER) cc_final: 0.8668 (p0) REVERT: A 357 TYR cc_start: 0.8711 (m-80) cc_final: 0.8361 (m-80) REVERT: A 413 MET cc_start: 0.8295 (mtm) cc_final: 0.8018 (mtt) REVERT: A 430 LYS cc_start: 0.9401 (ttmt) cc_final: 0.9105 (tptt) REVERT: C 90 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8010 (tp30) REVERT: C 156 ARG cc_start: 0.8772 (mmt90) cc_final: 0.8415 (mmm-85) REVERT: C 169 PHE cc_start: 0.8664 (m-80) cc_final: 0.8276 (m-80) REVERT: C 269 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8331 (pp) REVERT: C 327 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.8802 (p0) REVERT: C 358 GLN cc_start: 0.9314 (tp40) cc_final: 0.8954 (tp40) REVERT: C 417 GLU cc_start: 0.8470 (mp0) cc_final: 0.8157 (mp0) REVERT: E 6 SER cc_start: 0.9163 (m) cc_final: 0.8802 (p) REVERT: E 90 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7854 (tp30) REVERT: E 156 ARG cc_start: 0.8884 (mmt90) cc_final: 0.8607 (mmm-85) REVERT: E 269 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8566 (pp) REVERT: E 422 ARG cc_start: 0.8856 (tpt90) cc_final: 0.8544 (tpt-90) REVERT: E 430 LYS cc_start: 0.9449 (ttmt) cc_final: 0.9232 (tptt) REVERT: J 71 GLU cc_start: 0.8102 (pt0) cc_final: 0.7659 (tt0) REVERT: J 75 ILE cc_start: 0.9357 (mm) cc_final: 0.9000 (mt) REVERT: J 76 ASP cc_start: 0.8838 (m-30) cc_final: 0.8609 (m-30) REVERT: J 90 GLU cc_start: 0.8360 (tp30) cc_final: 0.7891 (tp30) REVERT: J 108 TYR cc_start: 0.9116 (m-80) cc_final: 0.8630 (m-80) REVERT: J 244 PHE cc_start: 0.8807 (m-80) cc_final: 0.8185 (m-80) REVERT: J 316 CYS cc_start: 0.8777 (t) cc_final: 0.8526 (t) REVERT: J 346 TRP cc_start: 0.8421 (p-90) cc_final: 0.4742 (t-100) REVERT: J 430 LYS cc_start: 0.9596 (ttmt) cc_final: 0.9280 (tptt) REVERT: J 432 TYR cc_start: 0.8650 (m-80) cc_final: 0.7884 (t80) REVERT: J 433 GLU cc_start: 0.9085 (tp30) cc_final: 0.8832 (tp30) REVERT: K 9 VAL cc_start: 0.9360 (t) cc_final: 0.9126 (p) REVERT: K 76 ASP cc_start: 0.8760 (m-30) cc_final: 0.8520 (m-30) REVERT: K 90 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7883 (tp30) REVERT: K 203 MET cc_start: 0.9233 (mmt) cc_final: 0.8924 (mmp) REVERT: K 256 GLN cc_start: 0.9067 (pt0) cc_final: 0.8651 (tm-30) REVERT: K 304 LYS cc_start: 0.8922 (tppp) cc_final: 0.8398 (tppp) REVERT: K 327 ASP cc_start: 0.9264 (OUTLIER) cc_final: 0.8842 (p0) REVERT: K 346 TRP cc_start: 0.8635 (p-90) cc_final: 0.4396 (t-100) REVERT: K 357 TYR cc_start: 0.8572 (m-80) cc_final: 0.8039 (m-80) REVERT: K 425 MET cc_start: 0.8728 (tpt) cc_final: 0.8491 (tpp) REVERT: K 430 LYS cc_start: 0.9525 (ttmt) cc_final: 0.9157 (tptt) REVERT: K 432 TYR cc_start: 0.8684 (m-80) cc_final: 0.7820 (t80) REVERT: K 433 GLU cc_start: 0.9173 (tt0) cc_final: 0.8885 (tp30) REVERT: L 69 ASP cc_start: 0.8454 (t0) cc_final: 0.8215 (t70) REVERT: L 90 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8236 (tp30) REVERT: L 109 THR cc_start: 0.8741 (m) cc_final: 0.8183 (p) REVERT: L 224 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7955 (m-10) REVERT: L 280 LYS cc_start: 0.3646 (mmtt) cc_final: 0.3337 (mmtt) REVERT: L 297 GLU cc_start: 0.9234 (tp30) cc_final: 0.9003 (tp30) REVERT: L 327 ASP cc_start: 0.9331 (OUTLIER) cc_final: 0.9037 (p0) REVERT: L 346 TRP cc_start: 0.8472 (p-90) cc_final: 0.4738 (t-100) REVERT: L 352 LYS cc_start: 0.2851 (mmtt) cc_final: 0.2114 (mmtm) REVERT: L 433 GLU cc_start: 0.9009 (tp30) cc_final: 0.8785 (tp30) REVERT: F 14 ASN cc_start: 0.8736 (m-40) cc_final: 0.8507 (m-40) REVERT: F 134 GLN cc_start: 0.8830 (pt0) cc_final: 0.8605 (pt0) REVERT: F 209 ASP cc_start: 0.8782 (t0) cc_final: 0.8581 (t70) REVERT: F 216 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8327 (ptpp) REVERT: F 226 ASN cc_start: 0.9231 (m-40) cc_final: 0.8897 (m-40) REVERT: F 310 TYR cc_start: 0.9152 (m-80) cc_final: 0.8859 (m-10) REVERT: F 375 GLN cc_start: 0.8415 (pp30) cc_final: 0.8065 (pp30) REVERT: F 395 LEU cc_start: 0.9231 (mm) cc_final: 0.8998 (mm) REVERT: F 405 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8121 (tm-30) REVERT: F 406 MET cc_start: 0.8693 (tpp) cc_final: 0.8335 (tpp) REVERT: D 6 HIS cc_start: 0.8594 (t-170) cc_final: 0.8262 (t-170) REVERT: D 8 GLN cc_start: 0.8485 (mt0) cc_final: 0.8132 (mt0) REVERT: D 22 GLU cc_start: 0.8364 (tm-30) cc_final: 0.7659 (tm-30) REVERT: D 26 ASP cc_start: 0.8475 (m-30) cc_final: 0.7953 (m-30) REVERT: D 73 MET cc_start: 0.8944 (mmm) cc_final: 0.8704 (mmm) REVERT: D 99 ASN cc_start: 0.8436 (t0) cc_final: 0.8105 (t0) REVERT: D 122 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.8970 (tppt) REVERT: D 194 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8492 (mm-30) REVERT: D 209 ASP cc_start: 0.8624 (t0) cc_final: 0.7605 (t0) REVERT: D 213 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8137 (ttp-110) REVERT: D 279 GLN cc_start: 0.8753 (pt0) cc_final: 0.8291 (pt0) REVERT: D 297 LYS cc_start: 0.8710 (tppt) cc_final: 0.7822 (tppt) REVERT: D 312 THR cc_start: 0.9373 (m) cc_final: 0.9146 (m) REVERT: D 323 MET cc_start: 0.8358 (mpp) cc_final: 0.7766 (mpp) REVERT: D 330 MET cc_start: 0.8792 (mmt) cc_final: 0.8539 (mmt) REVERT: D 375 GLN cc_start: 0.8574 (pp30) cc_final: 0.7115 (pp30) REVERT: D 379 LYS cc_start: 0.9335 (mtpt) cc_final: 0.8587 (mtmt) REVERT: D 405 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8134 (tm-30) REVERT: D 422 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8088 (t80) REVERT: G 8 GLN cc_start: 0.8591 (mt0) cc_final: 0.8300 (mt0) REVERT: G 14 ASN cc_start: 0.8942 (m-40) cc_final: 0.8660 (m-40) REVERT: G 31 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: G 50 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: G 67 ASP cc_start: 0.8644 (t0) cc_final: 0.8175 (t0) REVERT: G 121 ARG cc_start: 0.8816 (ttm110) cc_final: 0.8312 (mtm180) REVERT: G 143 THR cc_start: 0.8700 (m) cc_final: 0.8435 (m) REVERT: G 164 MET cc_start: 0.8207 (mtm) cc_final: 0.7908 (mtt) REVERT: G 194 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8741 (mt-10) REVERT: G 209 ASP cc_start: 0.8743 (t0) cc_final: 0.8277 (t0) REVERT: G 226 ASN cc_start: 0.9015 (m-40) cc_final: 0.8731 (m-40) REVERT: G 237 THR cc_start: 0.8940 (m) cc_final: 0.8184 (t) REVERT: G 297 LYS cc_start: 0.9018 (tppt) cc_final: 0.8692 (tppt) REVERT: G 306 ARG cc_start: 0.9192 (mtt90) cc_final: 0.8785 (mtm110) REVERT: G 310 TYR cc_start: 0.9094 (m-80) cc_final: 0.8711 (m-80) REVERT: G 325 GLU cc_start: 0.8623 (tt0) cc_final: 0.7931 (tt0) REVERT: G 337 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7925 (t0) REVERT: G 370 ASN cc_start: 0.8695 (t0) cc_final: 0.8431 (t0) REVERT: G 375 GLN cc_start: 0.8163 (pp30) cc_final: 0.7608 (pp30) REVERT: H 46 ARG cc_start: 0.8607 (mmt-90) cc_final: 0.8394 (mmm-85) REVERT: H 50 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: H 121 ARG cc_start: 0.8770 (ttm110) cc_final: 0.8386 (mtm180) REVERT: H 162 ARG cc_start: 0.8665 (mmp80) cc_final: 0.8444 (mmp80) REVERT: H 195 ASN cc_start: 0.9128 (m-40) cc_final: 0.8909 (m-40) REVERT: H 209 ASP cc_start: 0.8741 (t0) cc_final: 0.8506 (t0) REVERT: H 324 LYS cc_start: 0.9129 (tmtp) cc_final: 0.8694 (tptp) REVERT: H 375 GLN cc_start: 0.8272 (pp30) cc_final: 0.7882 (pp30) REVERT: H 388 MET cc_start: 0.8430 (mtp) cc_final: 0.8024 (mmt) REVERT: I 31 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8423 (m-30) REVERT: I 121 ARG cc_start: 0.8774 (ttm110) cc_final: 0.8373 (mtm180) REVERT: I 123 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8899 (mm-30) REVERT: I 194 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8875 (mt-10) REVERT: I 252 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8501 (mtpp) REVERT: I 291 GLN cc_start: 0.8642 (mp10) cc_final: 0.8346 (mp10) REVERT: I 299 MET cc_start: 0.8140 (mmm) cc_final: 0.7887 (mmp) REVERT: I 363 MET cc_start: 0.8300 (ptp) cc_final: 0.8006 (ptt) REVERT: B 50 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: B 57 HIS cc_start: 0.6291 (t-170) cc_final: 0.6060 (t70) REVERT: B 59 TYR cc_start: 0.7905 (m-80) cc_final: 0.7646 (m-80) REVERT: B 73 MET cc_start: 0.8749 (mmm) cc_final: 0.8503 (mtt) REVERT: B 99 ASN cc_start: 0.8654 (t0) cc_final: 0.8236 (t0) REVERT: B 121 ARG cc_start: 0.9029 (mtm-85) cc_final: 0.8729 (mtm-85) REVERT: B 159 TYR cc_start: 0.8358 (m-80) cc_final: 0.8098 (m-80) REVERT: B 164 MET cc_start: 0.8874 (tpp) cc_final: 0.8644 (tpp) REVERT: B 288 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8276 (mt-10) REVERT: B 327 ASP cc_start: 0.9037 (m-30) cc_final: 0.8811 (p0) REVERT: B 405 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 424 GLN cc_start: 0.8711 (tt0) cc_final: 0.8285 (tt0) outliers start: 313 outliers final: 200 residues processed: 1706 average time/residue: 0.2339 time to fit residues: 653.1868 Evaluate side-chains 1626 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 1407 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 296 PHE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 376 CYS Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 379 LYS Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 143 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 503 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 309 optimal weight: 3.9990 chunk 351 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 423 optimal weight: 7.9990 chunk 366 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 424 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** E 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 107 HIS ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 190 HIS ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS F 337 ASN F 423 GLN D 307 HIS D 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 307 HIS ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 298 ASN B 423 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.105004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.088671 restraints weight = 90487.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.091851 restraints weight = 44827.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.093994 restraints weight = 27305.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.095487 restraints weight = 18851.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096566 restraints weight = 14178.168| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 41998 Z= 0.216 Angle : 0.659 13.691 57035 Z= 0.341 Chirality : 0.046 0.258 6240 Planarity : 0.005 0.047 7411 Dihedral : 10.583 137.341 5893 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 7.49 % Allowed : 21.37 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.12), residues: 5136 helix: 1.06 (0.10), residues: 2466 sheet: -1.14 (0.18), residues: 816 loop : -1.73 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 339 TYR 0.044 0.002 TYR C 210 PHE 0.032 0.002 PHE L 255 TRP 0.012 0.001 TRP L 21 HIS 0.007 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00479 (41998) covalent geometry : angle 0.65919 (57035) hydrogen bonds : bond 0.04919 ( 2184) hydrogen bonds : angle 5.14002 ( 6354) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1807 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 331 poor density : 1476 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7797 (tp30) REVERT: A 96 LYS cc_start: 0.8764 (tppt) cc_final: 0.8440 (tppp) REVERT: A 103 TYR cc_start: 0.8814 (t80) cc_final: 0.8402 (t80) REVERT: A 120 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8149 (t70) REVERT: A 121 ARG cc_start: 0.8334 (mmm160) cc_final: 0.7913 (tpt170) REVERT: A 169 PHE cc_start: 0.8641 (m-80) cc_final: 0.8258 (m-80) REVERT: A 224 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 254 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: A 306 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7572 (p0) REVERT: A 309 HIS cc_start: 0.8004 (m90) cc_final: 0.7777 (m90) REVERT: A 327 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8666 (p0) REVERT: A 357 TYR cc_start: 0.8762 (m-80) cc_final: 0.8415 (m-80) REVERT: A 430 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9132 (tptt) REVERT: C 90 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8063 (tp30) REVERT: C 96 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8544 (mmmm) REVERT: C 169 PHE cc_start: 0.8700 (m-80) cc_final: 0.8336 (m-80) REVERT: C 269 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8481 (pp) REVERT: C 327 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.8790 (p0) REVERT: C 338 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8563 (ttmt) REVERT: C 358 GLN cc_start: 0.9342 (tp40) cc_final: 0.9004 (tp40) REVERT: C 417 GLU cc_start: 0.8585 (mp0) cc_final: 0.8234 (mp0) REVERT: E 6 SER cc_start: 0.9134 (m) cc_final: 0.8752 (p) REVERT: E 88 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.5015 (t70) REVERT: E 90 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7988 (tp30) REVERT: E 248 LEU cc_start: 0.9100 (tp) cc_final: 0.8797 (tt) REVERT: E 269 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8495 (pp) REVERT: E 327 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8769 (p0) REVERT: E 417 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8598 (mp0) REVERT: E 430 LYS cc_start: 0.9529 (ttmt) cc_final: 0.9268 (tptt) REVERT: J 69 ASP cc_start: 0.8521 (t0) cc_final: 0.8306 (t0) REVERT: J 71 GLU cc_start: 0.7805 (pt0) cc_final: 0.7277 (pt0) REVERT: J 75 ILE cc_start: 0.9384 (mm) cc_final: 0.9053 (mt) REVERT: J 76 ASP cc_start: 0.8865 (m-30) cc_final: 0.8626 (m-30) REVERT: J 88 HIS cc_start: 0.6930 (OUTLIER) cc_final: 0.5409 (t70) REVERT: J 90 GLU cc_start: 0.8309 (tp30) cc_final: 0.7910 (tp30) REVERT: J 108 TYR cc_start: 0.9200 (m-80) cc_final: 0.8660 (m-80) REVERT: J 244 PHE cc_start: 0.8832 (m-80) cc_final: 0.8273 (m-80) REVERT: J 346 TRP cc_start: 0.8425 (p-90) cc_final: 0.4654 (t-100) REVERT: J 351 PHE cc_start: 0.8106 (m-80) cc_final: 0.7753 (m-80) REVERT: J 372 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: J 430 LYS cc_start: 0.9614 (ttmt) cc_final: 0.9287 (tptt) REVERT: J 432 TYR cc_start: 0.8694 (m-80) cc_final: 0.7784 (t80) REVERT: J 433 GLU cc_start: 0.9082 (tp30) cc_final: 0.8809 (tp30) REVERT: K 9 VAL cc_start: 0.9369 (t) cc_final: 0.9148 (p) REVERT: K 90 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: K 211 ASP cc_start: 0.9247 (m-30) cc_final: 0.9046 (m-30) REVERT: K 256 GLN cc_start: 0.9089 (pt0) cc_final: 0.8748 (tm-30) REVERT: K 327 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8872 (p0) REVERT: K 346 TRP cc_start: 0.8548 (p-90) cc_final: 0.4262 (t-100) REVERT: K 357 TYR cc_start: 0.8598 (m-80) cc_final: 0.8085 (m-80) REVERT: K 430 LYS cc_start: 0.9557 (ttmt) cc_final: 0.9177 (tptt) REVERT: K 432 TYR cc_start: 0.8690 (m-80) cc_final: 0.7866 (t80) REVERT: K 433 GLU cc_start: 0.9179 (tt0) cc_final: 0.8869 (tp30) REVERT: L 69 ASP cc_start: 0.8428 (t0) cc_final: 0.8212 (t70) REVERT: L 90 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8016 (tp30) REVERT: L 96 LYS cc_start: 0.8965 (tppt) cc_final: 0.8588 (tptp) REVERT: L 109 THR cc_start: 0.8758 (m) cc_final: 0.8271 (p) REVERT: L 224 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7968 (m-10) REVERT: L 280 LYS cc_start: 0.3362 (mmtt) cc_final: 0.2948 (tptt) REVERT: L 297 GLU cc_start: 0.9243 (tp30) cc_final: 0.9008 (tp30) REVERT: L 302 MET cc_start: 0.8511 (mtp) cc_final: 0.8300 (mtp) REVERT: L 327 ASP cc_start: 0.9340 (OUTLIER) cc_final: 0.9116 (p0) REVERT: L 346 TRP cc_start: 0.8517 (p-90) cc_final: 0.4738 (t-100) REVERT: L 394 LYS cc_start: 0.9241 (mppt) cc_final: 0.8843 (mppt) REVERT: L 433 GLU cc_start: 0.9020 (tp30) cc_final: 0.8811 (tp30) REVERT: F 8 GLN cc_start: 0.8815 (mt0) cc_final: 0.8288 (mt0) REVERT: F 14 ASN cc_start: 0.8808 (m-40) cc_final: 0.8491 (m-40) REVERT: F 162 ARG cc_start: 0.8556 (tpp-160) cc_final: 0.8183 (tpp-160) REVERT: F 213 ARG cc_start: 0.8436 (ttp-110) cc_final: 0.8201 (ttp-110) REVERT: F 310 TYR cc_start: 0.9189 (m-80) cc_final: 0.8829 (m-80) REVERT: F 320 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7214 (tpp-160) REVERT: F 329 GLN cc_start: 0.9287 (tp40) cc_final: 0.9084 (mm-40) REVERT: F 330 MET cc_start: 0.8786 (mmt) cc_final: 0.8540 (mmt) REVERT: F 375 GLN cc_start: 0.8449 (pp30) cc_final: 0.8029 (pp30) REVERT: F 395 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8997 (mm) REVERT: F 405 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8117 (tm-30) REVERT: F 406 MET cc_start: 0.8684 (tpp) cc_final: 0.8357 (tpp) REVERT: D 6 HIS cc_start: 0.8575 (t-170) cc_final: 0.8307 (t70) REVERT: D 8 GLN cc_start: 0.8422 (mt0) cc_final: 0.8037 (mt0) REVERT: D 22 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7865 (tm-30) REVERT: D 26 ASP cc_start: 0.8443 (m-30) cc_final: 0.8029 (m-30) REVERT: D 73 MET cc_start: 0.8892 (mmm) cc_final: 0.8642 (mmm) REVERT: D 99 ASN cc_start: 0.8512 (t0) cc_final: 0.8132 (t0) REVERT: D 122 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.8985 (tppt) REVERT: D 194 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8455 (mm-30) REVERT: D 209 ASP cc_start: 0.8557 (t0) cc_final: 0.7388 (t0) REVERT: D 213 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8198 (ttp-110) REVERT: D 279 GLN cc_start: 0.8778 (pt0) cc_final: 0.8232 (pt0) REVERT: D 297 LYS cc_start: 0.8855 (tppt) cc_final: 0.7949 (tppt) REVERT: D 321 MET cc_start: 0.8765 (ptp) cc_final: 0.8496 (ptp) REVERT: D 323 MET cc_start: 0.8363 (mpp) cc_final: 0.7741 (mpp) REVERT: D 329 GLN cc_start: 0.8994 (tp40) cc_final: 0.8770 (tp40) REVERT: D 330 MET cc_start: 0.8824 (mmt) cc_final: 0.8566 (mmt) REVERT: D 375 GLN cc_start: 0.8516 (pp30) cc_final: 0.7322 (pp30) REVERT: D 379 LYS cc_start: 0.9396 (mtpt) cc_final: 0.8686 (mtpt) REVERT: D 405 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8178 (tm-30) REVERT: D 422 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8063 (t80) REVERT: G 8 GLN cc_start: 0.8580 (mt0) cc_final: 0.8217 (mt0) REVERT: G 31 ASP cc_start: 0.8814 (m-30) cc_final: 0.8503 (m-30) REVERT: G 50 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7798 (m-80) REVERT: G 67 ASP cc_start: 0.8600 (t0) cc_final: 0.8287 (t0) REVERT: G 84 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8220 (pt) REVERT: G 121 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8373 (mtm180) REVERT: G 164 MET cc_start: 0.8234 (mtm) cc_final: 0.8021 (mtt) REVERT: G 194 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8747 (mt-10) REVERT: G 209 ASP cc_start: 0.8749 (t0) cc_final: 0.8277 (t0) REVERT: G 226 ASN cc_start: 0.8999 (m-40) cc_final: 0.8724 (m-40) REVERT: G 237 THR cc_start: 0.8885 (m) cc_final: 0.8260 (t) REVERT: G 297 LYS cc_start: 0.9044 (tppt) cc_final: 0.8691 (tppt) REVERT: G 304 ASP cc_start: 0.8581 (t0) cc_final: 0.8328 (t0) REVERT: G 306 ARG cc_start: 0.9201 (mtt90) cc_final: 0.8874 (mtm-85) REVERT: G 310 TYR cc_start: 0.9126 (m-80) cc_final: 0.8723 (m-80) REVERT: G 324 LYS cc_start: 0.9219 (tmtp) cc_final: 0.8993 (tttp) REVERT: G 379 LYS cc_start: 0.9463 (mtpt) cc_final: 0.8932 (mtmm) REVERT: H 46 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8438 (mmm-85) REVERT: H 50 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: H 67 ASP cc_start: 0.8496 (t0) cc_final: 0.7990 (t70) REVERT: H 73 MET cc_start: 0.8901 (mmm) cc_final: 0.8453 (mtm) REVERT: H 121 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8410 (mtm180) REVERT: H 195 ASN cc_start: 0.9160 (m-40) cc_final: 0.8884 (m-40) REVERT: H 249 ASP cc_start: 0.8361 (p0) cc_final: 0.7872 (p0) REVERT: H 324 LYS cc_start: 0.8994 (tmtp) cc_final: 0.8721 (tptp) REVERT: H 388 MET cc_start: 0.8421 (mtp) cc_final: 0.8008 (mmt) REVERT: H 426 GLN cc_start: 0.7866 (tt0) cc_final: 0.7590 (tp40) REVERT: I 31 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8473 (m-30) REVERT: I 67 ASP cc_start: 0.8267 (t0) cc_final: 0.8003 (t0) REVERT: I 121 ARG cc_start: 0.8803 (ttm110) cc_final: 0.8356 (mtm180) REVERT: I 123 GLU cc_start: 0.9467 (mm-30) cc_final: 0.8828 (mm-30) REVERT: I 299 MET cc_start: 0.8065 (mmm) cc_final: 0.7566 (mmm) REVERT: I 375 GLN cc_start: 0.8302 (pp30) cc_final: 0.7909 (pp30) REVERT: B 73 MET cc_start: 0.8597 (mmm) cc_final: 0.8222 (mtt) REVERT: B 99 ASN cc_start: 0.8695 (t0) cc_final: 0.8096 (t0) REVERT: B 164 MET cc_start: 0.8993 (tpp) cc_final: 0.8756 (tpp) REVERT: B 329 GLN cc_start: 0.8943 (mm110) cc_final: 0.8701 (tp40) REVERT: B 370 ASN cc_start: 0.8041 (t0) cc_final: 0.7463 (t0) REVERT: B 405 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 424 GLN cc_start: 0.8766 (tt0) cc_final: 0.8256 (tt0) outliers start: 331 outliers final: 225 residues processed: 1678 average time/residue: 0.2304 time to fit residues: 632.8031 Evaluate side-chains 1642 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 1392 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 129 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 36 MET Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 78 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 237 SER Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 372 GLN Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 129 CYS Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 391 LEU Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 129 CYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 213 CYS Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 339 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 282 ARG Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 144 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 310 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 483 optimal weight: 1.9990 chunk 416 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 88 HIS ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN C 301 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN J 101 ASN J 128 GLN ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS K 11 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 258 ASN K 300 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS D 227 HIS D 307 HIS ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN G 307 HIS G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS I 307 HIS I 334 GLN ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 307 HIS B 423 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.104485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087963 restraints weight = 91122.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.091174 restraints weight = 45335.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093361 restraints weight = 27502.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094892 restraints weight = 18845.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.095980 restraints weight = 14081.989| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41998 Z= 0.187 Angle : 0.660 13.659 57035 Z= 0.339 Chirality : 0.046 0.267 6240 Planarity : 0.005 0.068 7411 Dihedral : 10.432 136.850 5888 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 7.02 % Allowed : 22.78 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 5136 helix: 1.01 (0.10), residues: 2496 sheet: -0.84 (0.19), residues: 774 loop : -1.86 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 339 TYR 0.045 0.001 TYR C 210 PHE 0.045 0.002 PHE L 255 TRP 0.013 0.001 TRP L 21 HIS 0.006 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00417 (41998) covalent geometry : angle 0.66031 (57035) hydrogen bonds : bond 0.04706 ( 2184) hydrogen bonds : angle 5.03836 ( 6354) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1782 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 310 poor density : 1472 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7619 (tm-30) REVERT: A 96 LYS cc_start: 0.8752 (tppt) cc_final: 0.8442 (tppp) REVERT: A 120 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8155 (t0) REVERT: A 121 ARG cc_start: 0.8275 (mmm160) cc_final: 0.7746 (tpt170) REVERT: A 169 PHE cc_start: 0.8670 (m-80) cc_final: 0.8458 (m-80) REVERT: A 214 ARG cc_start: 0.8646 (tmm-80) cc_final: 0.8276 (tmm-80) REVERT: A 224 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: A 254 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: A 306 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7348 (p0) REVERT: A 309 HIS cc_start: 0.8013 (m90) cc_final: 0.7729 (m90) REVERT: A 327 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8736 (p0) REVERT: A 357 TYR cc_start: 0.8780 (m-80) cc_final: 0.8394 (m-80) REVERT: A 386 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7366 (pt0) REVERT: A 430 LYS cc_start: 0.9441 (ttmt) cc_final: 0.9128 (tptt) REVERT: C 90 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8085 (tp30) REVERT: C 96 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8575 (mmtp) REVERT: C 169 PHE cc_start: 0.8723 (m-80) cc_final: 0.8368 (m-80) REVERT: C 269 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 327 ASP cc_start: 0.9282 (OUTLIER) cc_final: 0.8785 (p0) REVERT: C 338 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8617 (ttmt) REVERT: C 358 GLN cc_start: 0.9347 (tp40) cc_final: 0.9015 (tp40) REVERT: C 417 GLU cc_start: 0.8684 (mp0) cc_final: 0.8290 (mp0) REVERT: E 88 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.4919 (t70) REVERT: E 90 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7975 (tp30) REVERT: E 214 ARG cc_start: 0.8855 (tmm-80) cc_final: 0.8156 (tmm-80) REVERT: E 248 LEU cc_start: 0.9080 (tp) cc_final: 0.8799 (tt) REVERT: E 269 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8509 (pp) REVERT: E 327 ASP cc_start: 0.9161 (OUTLIER) cc_final: 0.8760 (p0) REVERT: E 332 ILE cc_start: 0.9644 (OUTLIER) cc_final: 0.9411 (mp) REVERT: E 351 PHE cc_start: 0.8069 (m-80) cc_final: 0.7845 (m-80) REVERT: E 430 LYS cc_start: 0.9543 (ttmt) cc_final: 0.9255 (tptt) REVERT: J 69 ASP cc_start: 0.8719 (t0) cc_final: 0.8487 (t0) REVERT: J 71 GLU cc_start: 0.7922 (pt0) cc_final: 0.7586 (pt0) REVERT: J 75 ILE cc_start: 0.9373 (mm) cc_final: 0.9022 (mt) REVERT: J 76 ASP cc_start: 0.8847 (m-30) cc_final: 0.8618 (m-30) REVERT: J 88 HIS cc_start: 0.6674 (OUTLIER) cc_final: 0.5096 (t70) REVERT: J 90 GLU cc_start: 0.8340 (tp30) cc_final: 0.7952 (tp30) REVERT: J 108 TYR cc_start: 0.9164 (m-80) cc_final: 0.8725 (m-80) REVERT: J 109 THR cc_start: 0.9024 (m) cc_final: 0.8814 (p) REVERT: J 308 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8199 (ptp90) REVERT: J 339 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7676 (ptm160) REVERT: J 346 TRP cc_start: 0.8516 (p-90) cc_final: 0.4640 (t-100) REVERT: J 413 MET cc_start: 0.8667 (tpp) cc_final: 0.8431 (mmm) REVERT: J 423 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8933 (mt-10) REVERT: J 430 LYS cc_start: 0.9602 (ttmt) cc_final: 0.9255 (tptt) REVERT: J 432 TYR cc_start: 0.8641 (m-80) cc_final: 0.7974 (t80) REVERT: K 3 GLU cc_start: 0.7491 (mp0) cc_final: 0.7239 (mm-30) REVERT: K 9 VAL cc_start: 0.9357 (t) cc_final: 0.9153 (p) REVERT: K 69 ASP cc_start: 0.8634 (t0) cc_final: 0.8400 (t0) REVERT: K 71 GLU cc_start: 0.8188 (tt0) cc_final: 0.7883 (tt0) REVERT: K 90 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: K 108 TYR cc_start: 0.8989 (m-80) cc_final: 0.7937 (m-10) REVERT: K 211 ASP cc_start: 0.9313 (m-30) cc_final: 0.9060 (m-30) REVERT: K 256 GLN cc_start: 0.9063 (pt0) cc_final: 0.8741 (tm-30) REVERT: K 327 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.8895 (p0) REVERT: K 346 TRP cc_start: 0.8539 (p-90) cc_final: 0.4272 (t-100) REVERT: K 357 TYR cc_start: 0.8632 (m-80) cc_final: 0.8045 (m-80) REVERT: K 386 GLU cc_start: 0.8652 (tt0) cc_final: 0.8252 (pt0) REVERT: K 430 LYS cc_start: 0.9571 (ttmt) cc_final: 0.9176 (tptt) REVERT: K 432 TYR cc_start: 0.8689 (m-80) cc_final: 0.7910 (t80) REVERT: K 433 GLU cc_start: 0.9163 (tt0) cc_final: 0.8867 (tp30) REVERT: L 71 GLU cc_start: 0.7767 (pt0) cc_final: 0.7480 (tt0) REVERT: L 76 ASP cc_start: 0.8881 (m-30) cc_final: 0.8633 (m-30) REVERT: L 90 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: L 109 THR cc_start: 0.8654 (m) cc_final: 0.8270 (p) REVERT: L 224 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7896 (m-10) REVERT: L 232 SER cc_start: 0.9205 (m) cc_final: 0.8805 (p) REVERT: L 346 TRP cc_start: 0.8585 (p-90) cc_final: 0.4757 (t-100) REVERT: L 352 LYS cc_start: 0.2632 (mmtt) cc_final: 0.2265 (mptt) REVERT: L 394 LYS cc_start: 0.9242 (mppt) cc_final: 0.8862 (mppt) REVERT: L 417 GLU cc_start: 0.8095 (mp0) cc_final: 0.7856 (mp0) REVERT: F 2 ARG cc_start: 0.8468 (mtm180) cc_final: 0.8092 (mtm180) REVERT: F 8 GLN cc_start: 0.8704 (mt0) cc_final: 0.8026 (mt0) REVERT: F 14 ASN cc_start: 0.8790 (m-40) cc_final: 0.8472 (m-40) REVERT: F 167 PHE cc_start: 0.8337 (m-10) cc_final: 0.8124 (m-80) REVERT: F 213 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8309 (ttp-110) REVERT: F 226 ASN cc_start: 0.9215 (m-40) cc_final: 0.8867 (m-40) REVERT: F 310 TYR cc_start: 0.9183 (m-80) cc_final: 0.8929 (m-80) REVERT: F 329 GLN cc_start: 0.9279 (tp40) cc_final: 0.8971 (tp40) REVERT: F 330 MET cc_start: 0.8807 (mmt) cc_final: 0.8508 (mmt) REVERT: F 375 GLN cc_start: 0.8462 (pp30) cc_final: 0.7997 (pp30) REVERT: F 405 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8135 (tm-30) REVERT: F 406 MET cc_start: 0.8650 (tpp) cc_final: 0.7775 (tpp) REVERT: F 410 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8651 (mt-10) REVERT: D 22 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7727 (tm-30) REVERT: D 26 ASP cc_start: 0.8480 (m-30) cc_final: 0.7912 (m-30) REVERT: D 73 MET cc_start: 0.8910 (mmm) cc_final: 0.8662 (mmm) REVERT: D 99 ASN cc_start: 0.8464 (t0) cc_final: 0.8105 (t0) REVERT: D 108 GLU cc_start: 0.8279 (tp30) cc_final: 0.8076 (tp30) REVERT: D 122 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9014 (tppt) REVERT: D 194 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8414 (mm-30) REVERT: D 279 GLN cc_start: 0.8808 (pt0) cc_final: 0.8348 (pt0) REVERT: D 323 MET cc_start: 0.8351 (mpp) cc_final: 0.7712 (mpp) REVERT: D 329 GLN cc_start: 0.9035 (tp40) cc_final: 0.8705 (tp40) REVERT: D 330 MET cc_start: 0.8822 (mmt) cc_final: 0.8565 (mmt) REVERT: D 344 TRP cc_start: 0.9012 (OUTLIER) cc_final: 0.7915 (p-90) REVERT: D 375 GLN cc_start: 0.8519 (pp30) cc_final: 0.7208 (pp30) REVERT: D 379 LYS cc_start: 0.9416 (mtpt) cc_final: 0.8671 (mtmt) REVERT: D 405 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8177 (tm-30) REVERT: D 422 TYR cc_start: 0.9070 (OUTLIER) cc_final: 0.7993 (t80) REVERT: G 8 GLN cc_start: 0.8511 (mt0) cc_final: 0.8223 (mt0) REVERT: G 50 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7793 (m-80) REVERT: G 67 ASP cc_start: 0.8581 (t0) cc_final: 0.8291 (t0) REVERT: G 121 ARG cc_start: 0.8890 (ttm110) cc_final: 0.8428 (mtm180) REVERT: G 143 THR cc_start: 0.8536 (m) cc_final: 0.8304 (m) REVERT: G 164 MET cc_start: 0.8335 (mtm) cc_final: 0.8063 (mtt) REVERT: G 226 ASN cc_start: 0.8965 (m-40) cc_final: 0.8666 (m-40) REVERT: G 237 THR cc_start: 0.8793 (m) cc_final: 0.8428 (m) REVERT: G 276 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7720 (mmm160) REVERT: G 297 LYS cc_start: 0.9024 (tppt) cc_final: 0.8657 (tppt) REVERT: G 306 ARG cc_start: 0.9210 (mtt90) cc_final: 0.8779 (mtm110) REVERT: G 310 TYR cc_start: 0.9131 (m-80) cc_final: 0.8749 (m-80) REVERT: G 375 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7565 (pp30) REVERT: H 46 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8388 (mmm-85) REVERT: H 50 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: H 73 MET cc_start: 0.8853 (mmm) cc_final: 0.8472 (mtm) REVERT: H 111 GLU cc_start: 0.8800 (mp0) cc_final: 0.8553 (mp0) REVERT: H 121 ARG cc_start: 0.8813 (ttm110) cc_final: 0.8450 (mtm180) REVERT: H 195 ASN cc_start: 0.9167 (m-40) cc_final: 0.8881 (m-40) REVERT: H 249 ASP cc_start: 0.8370 (p0) cc_final: 0.7811 (p0) REVERT: H 329 GLN cc_start: 0.9216 (mm110) cc_final: 0.8649 (mm-40) REVERT: H 364 SER cc_start: 0.8984 (p) cc_final: 0.8638 (p) REVERT: H 388 MET cc_start: 0.8460 (mtp) cc_final: 0.8025 (mmt) REVERT: I 31 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: I 121 ARG cc_start: 0.8838 (ttm110) cc_final: 0.8414 (mtm180) REVERT: I 123 GLU cc_start: 0.9471 (mm-30) cc_final: 0.8815 (mm-30) REVERT: I 279 GLN cc_start: 0.8653 (pt0) cc_final: 0.8147 (pt0) REVERT: I 363 MET cc_start: 0.8323 (ptp) cc_final: 0.7833 (ptt) REVERT: I 375 GLN cc_start: 0.8320 (pp30) cc_final: 0.7875 (pp30) REVERT: B 50 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: B 73 MET cc_start: 0.8555 (mmm) cc_final: 0.8175 (mtt) REVERT: B 99 ASN cc_start: 0.8756 (t0) cc_final: 0.8008 (t0) REVERT: B 122 LYS cc_start: 0.9092 (pttp) cc_final: 0.8814 (ptmm) REVERT: B 164 MET cc_start: 0.9016 (tpp) cc_final: 0.8803 (tpp) REVERT: B 327 ASP cc_start: 0.9119 (m-30) cc_final: 0.8893 (p0) REVERT: B 329 GLN cc_start: 0.8955 (mm110) cc_final: 0.8704 (tp40) REVERT: B 370 ASN cc_start: 0.8035 (t0) cc_final: 0.7480 (t0) REVERT: B 405 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 424 GLN cc_start: 0.8839 (tt0) cc_final: 0.8319 (tt0) outliers start: 310 outliers final: 218 residues processed: 1661 average time/residue: 0.2314 time to fit residues: 630.8292 Evaluate side-chains 1660 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 245 poor density : 1415 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 129 CYS Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 308 ARG Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 213 CYS Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 172 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 266 PHE Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 129 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 222 optimal weight: 10.0000 chunk 445 optimal weight: 6.9990 chunk 288 optimal weight: 9.9990 chunk 280 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 345 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 300 optimal weight: 20.0000 chunk 421 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 285 GLN E 31 GLN E 256 GLN E 258 ASN E 309 HIS ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS K 11 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN K 128 GLN K 300 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 HIS F 256 ASN ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS D 307 HIS ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN I 307 HIS ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 307 HIS B 423 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.105347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.088743 restraints weight = 91072.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091976 restraints weight = 45273.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.094184 restraints weight = 27506.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.095743 restraints weight = 18851.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096849 restraints weight = 14081.491| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 41998 Z= 0.162 Angle : 0.667 14.745 57035 Z= 0.339 Chirality : 0.046 0.263 6240 Planarity : 0.005 0.053 7411 Dihedral : 10.222 136.487 5871 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.36 % Favored : 95.62 % Rotamer: Outliers : 6.27 % Allowed : 24.77 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 5136 helix: 1.06 (0.10), residues: 2502 sheet: -0.66 (0.19), residues: 798 loop : -1.77 (0.15), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 339 TYR 0.049 0.001 TYR C 210 PHE 0.044 0.002 PHE L 255 TRP 0.011 0.001 TRP G 21 HIS 0.008 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00362 (41998) covalent geometry : angle 0.66746 (57035) hydrogen bonds : bond 0.04508 ( 2184) hydrogen bonds : angle 4.98757 ( 6354) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1779 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 1502 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7820 (tm-30) REVERT: A 96 LYS cc_start: 0.8720 (tppt) cc_final: 0.8382 (tppp) REVERT: A 103 TYR cc_start: 0.8660 (t80) cc_final: 0.8322 (t80) REVERT: A 120 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8167 (t0) REVERT: A 121 ARG cc_start: 0.8247 (mmm160) cc_final: 0.7874 (tpt170) REVERT: A 214 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8238 (tmm-80) REVERT: A 224 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: A 254 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: A 306 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.6940 (p0) REVERT: A 309 HIS cc_start: 0.8013 (m90) cc_final: 0.7663 (m90) REVERT: A 327 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8726 (p0) REVERT: A 357 TYR cc_start: 0.8754 (m-80) cc_final: 0.8356 (m-80) REVERT: A 386 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: A 430 LYS cc_start: 0.9408 (ttmt) cc_final: 0.9141 (tptt) REVERT: C 90 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8053 (tp30) REVERT: C 145 THR cc_start: 0.7804 (m) cc_final: 0.7376 (m) REVERT: C 169 PHE cc_start: 0.8691 (m-80) cc_final: 0.8386 (m-80) REVERT: C 256 GLN cc_start: 0.9418 (pt0) cc_final: 0.8972 (pm20) REVERT: C 269 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8378 (pp) REVERT: C 327 ASP cc_start: 0.9279 (OUTLIER) cc_final: 0.8784 (p0) REVERT: C 358 GLN cc_start: 0.9345 (tp40) cc_final: 0.9007 (tp40) REVERT: C 417 GLU cc_start: 0.8655 (mp0) cc_final: 0.8262 (mp0) REVERT: E 88 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.4645 (t70) REVERT: E 90 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7956 (tp30) REVERT: E 210 TYR cc_start: 0.8928 (m-10) cc_final: 0.8661 (m-80) REVERT: E 214 ARG cc_start: 0.8896 (tmm-80) cc_final: 0.8220 (tmm-80) REVERT: E 248 LEU cc_start: 0.9056 (tp) cc_final: 0.8759 (tt) REVERT: E 269 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8567 (pp) REVERT: E 327 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8806 (p0) REVERT: E 332 ILE cc_start: 0.9643 (OUTLIER) cc_final: 0.9402 (mp) REVERT: E 351 PHE cc_start: 0.8062 (m-80) cc_final: 0.7836 (m-80) REVERT: E 430 LYS cc_start: 0.9548 (ttmt) cc_final: 0.9253 (tptt) REVERT: J 71 GLU cc_start: 0.7907 (pt0) cc_final: 0.7684 (pt0) REVERT: J 75 ILE cc_start: 0.9353 (mm) cc_final: 0.8981 (mt) REVERT: J 76 ASP cc_start: 0.8827 (m-30) cc_final: 0.8595 (m-30) REVERT: J 88 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.5140 (t70) REVERT: J 90 GLU cc_start: 0.8363 (tp30) cc_final: 0.7976 (tp30) REVERT: J 108 TYR cc_start: 0.9111 (m-80) cc_final: 0.8737 (m-80) REVERT: J 244 PHE cc_start: 0.8774 (m-80) cc_final: 0.8294 (m-80) REVERT: J 248 LEU cc_start: 0.8852 (tp) cc_final: 0.8446 (tt) REVERT: J 308 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8167 (ptp90) REVERT: J 339 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7643 (ptm160) REVERT: J 346 TRP cc_start: 0.8530 (p-90) cc_final: 0.4578 (t-100) REVERT: J 413 MET cc_start: 0.8652 (tpp) cc_final: 0.8441 (mmm) REVERT: J 423 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8924 (mt-10) REVERT: J 430 LYS cc_start: 0.9595 (ttmt) cc_final: 0.9251 (tptt) REVERT: J 432 TYR cc_start: 0.8651 (m-80) cc_final: 0.8004 (t80) REVERT: K 3 GLU cc_start: 0.7542 (mp0) cc_final: 0.7249 (mm-30) REVERT: K 6 SER cc_start: 0.8935 (m) cc_final: 0.8644 (t) REVERT: K 69 ASP cc_start: 0.8639 (t0) cc_final: 0.8356 (t0) REVERT: K 71 GLU cc_start: 0.8106 (tt0) cc_final: 0.7760 (tt0) REVERT: K 90 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: K 108 TYR cc_start: 0.9054 (m-80) cc_final: 0.8124 (m-10) REVERT: K 211 ASP cc_start: 0.9313 (m-30) cc_final: 0.9058 (m-30) REVERT: K 256 GLN cc_start: 0.9086 (pt0) cc_final: 0.8722 (tm-30) REVERT: K 287 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8213 (p) REVERT: K 300 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8756 (t0) REVERT: K 346 TRP cc_start: 0.8559 (p-90) cc_final: 0.4152 (t-100) REVERT: K 357 TYR cc_start: 0.8628 (m-80) cc_final: 0.8061 (m-80) REVERT: K 386 GLU cc_start: 0.8653 (tt0) cc_final: 0.8246 (pt0) REVERT: K 422 ARG cc_start: 0.9130 (tpt90) cc_final: 0.8847 (tpt170) REVERT: K 430 LYS cc_start: 0.9557 (ttmt) cc_final: 0.9142 (tptt) REVERT: K 432 TYR cc_start: 0.8667 (m-80) cc_final: 0.7784 (t80) REVERT: K 433 GLU cc_start: 0.9136 (tt0) cc_final: 0.8855 (tp30) REVERT: L 76 ASP cc_start: 0.8896 (m-30) cc_final: 0.8628 (m-30) REVERT: L 90 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8151 (tp30) REVERT: L 109 THR cc_start: 0.8672 (m) cc_final: 0.8177 (p) REVERT: L 224 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7821 (m-10) REVERT: L 232 SER cc_start: 0.9253 (m) cc_final: 0.8855 (p) REVERT: L 346 TRP cc_start: 0.8587 (p-90) cc_final: 0.4642 (t-100) REVERT: L 352 LYS cc_start: 0.2535 (mmtt) cc_final: 0.2232 (mptt) REVERT: L 372 GLN cc_start: 0.8825 (mp10) cc_final: 0.8542 (pm20) REVERT: L 394 LYS cc_start: 0.9259 (mppt) cc_final: 0.8897 (mppt) REVERT: L 417 GLU cc_start: 0.7988 (mp0) cc_final: 0.7782 (mp0) REVERT: F 2 ARG cc_start: 0.8446 (mtm180) cc_final: 0.7924 (mtm180) REVERT: F 8 GLN cc_start: 0.8631 (mt0) cc_final: 0.8158 (mt0) REVERT: F 14 ASN cc_start: 0.8794 (m-40) cc_final: 0.8477 (m-40) REVERT: F 159 TYR cc_start: 0.8659 (m-80) cc_final: 0.8126 (m-80) REVERT: F 167 PHE cc_start: 0.8369 (m-10) cc_final: 0.6885 (m-80) REVERT: F 226 ASN cc_start: 0.9204 (m-40) cc_final: 0.8832 (m-40) REVERT: F 245 GLN cc_start: 0.8609 (mp10) cc_final: 0.8260 (mp10) REVERT: F 299 MET cc_start: 0.8319 (mmp) cc_final: 0.8072 (mmp) REVERT: F 310 TYR cc_start: 0.9183 (m-80) cc_final: 0.8947 (m-80) REVERT: F 325 GLU cc_start: 0.8782 (tt0) cc_final: 0.8287 (pt0) REVERT: F 329 GLN cc_start: 0.9280 (tp40) cc_final: 0.8970 (tp40) REVERT: F 330 MET cc_start: 0.8794 (mmt) cc_final: 0.8515 (mmt) REVERT: F 370 ASN cc_start: 0.8211 (t0) cc_final: 0.8004 (t0) REVERT: F 375 GLN cc_start: 0.8466 (pp30) cc_final: 0.7454 (pp30) REVERT: F 395 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8997 (mm) REVERT: F 405 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8171 (tm-30) REVERT: F 406 MET cc_start: 0.8628 (tpp) cc_final: 0.7698 (tpp) REVERT: F 410 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8592 (mt-10) REVERT: D 22 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7858 (tm-30) REVERT: D 26 ASP cc_start: 0.8490 (m-30) cc_final: 0.7983 (m-30) REVERT: D 99 ASN cc_start: 0.8454 (t0) cc_final: 0.8089 (t0) REVERT: D 108 GLU cc_start: 0.8287 (tp30) cc_final: 0.8075 (tp30) REVERT: D 122 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9022 (tppt) REVERT: D 156 ARG cc_start: 0.8111 (tpp-160) cc_final: 0.6805 (tpp-160) REVERT: D 159 TYR cc_start: 0.8541 (m-80) cc_final: 0.7786 (m-10) REVERT: D 194 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8391 (mm-30) REVERT: D 213 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8280 (ttp-110) REVERT: D 279 GLN cc_start: 0.8727 (pt0) cc_final: 0.8278 (pt0) REVERT: D 297 LYS cc_start: 0.8933 (tppt) cc_final: 0.8224 (tppt) REVERT: D 323 MET cc_start: 0.8281 (mpp) cc_final: 0.7509 (mpp) REVERT: D 329 GLN cc_start: 0.9089 (tp40) cc_final: 0.8711 (tp40) REVERT: D 330 MET cc_start: 0.8812 (mmt) cc_final: 0.8576 (mmt) REVERT: D 344 TRP cc_start: 0.8983 (OUTLIER) cc_final: 0.7951 (p-90) REVERT: D 375 GLN cc_start: 0.8483 (pp30) cc_final: 0.7181 (pp30) REVERT: D 376 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8005 (mt-10) REVERT: D 379 LYS cc_start: 0.9429 (mtpt) cc_final: 0.8769 (mtmt) REVERT: D 405 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8180 (tm-30) REVERT: D 422 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8072 (t80) REVERT: G 31 ASP cc_start: 0.8844 (m-30) cc_final: 0.8500 (m-30) REVERT: G 50 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: G 101 TRP cc_start: 0.9188 (t60) cc_final: 0.8971 (t60) REVERT: G 121 ARG cc_start: 0.8885 (ttm110) cc_final: 0.8425 (mtm180) REVERT: G 143 THR cc_start: 0.8556 (m) cc_final: 0.8304 (m) REVERT: G 156 ARG cc_start: 0.8284 (ttt180) cc_final: 0.8055 (ttt180) REVERT: G 209 ASP cc_start: 0.8909 (p0) cc_final: 0.8578 (p0) REVERT: G 226 ASN cc_start: 0.8935 (m-40) cc_final: 0.8649 (m-40) REVERT: G 237 THR cc_start: 0.8719 (m) cc_final: 0.8441 (m) REVERT: G 276 ARG cc_start: 0.8139 (mmm160) cc_final: 0.7812 (mmm160) REVERT: G 291 GLN cc_start: 0.8853 (mp10) cc_final: 0.8544 (mp10) REVERT: G 297 LYS cc_start: 0.9060 (tppt) cc_final: 0.8701 (tppt) REVERT: G 310 TYR cc_start: 0.9131 (m-10) cc_final: 0.8828 (m-80) REVERT: G 375 GLN cc_start: 0.8420 (pp30) cc_final: 0.7992 (pp30) REVERT: H 31 ASP cc_start: 0.8248 (m-30) cc_final: 0.8022 (m-30) REVERT: H 50 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: H 67 ASP cc_start: 0.8317 (t0) cc_final: 0.8062 (t0) REVERT: H 73 MET cc_start: 0.8724 (mmm) cc_final: 0.8402 (mtm) REVERT: H 111 GLU cc_start: 0.8847 (mp0) cc_final: 0.8583 (mp0) REVERT: H 121 ARG cc_start: 0.8848 (ttm110) cc_final: 0.8545 (mtm180) REVERT: H 195 ASN cc_start: 0.9167 (m-40) cc_final: 0.8894 (m-40) REVERT: H 208 TYR cc_start: 0.9025 (m-10) cc_final: 0.8414 (m-80) REVERT: H 249 ASP cc_start: 0.8320 (p0) cc_final: 0.7836 (p0) REVERT: H 329 GLN cc_start: 0.9189 (mm110) cc_final: 0.8631 (mm-40) REVERT: H 344 TRP cc_start: 0.9133 (OUTLIER) cc_final: 0.8423 (p-90) REVERT: H 364 SER cc_start: 0.8989 (p) cc_final: 0.8611 (p) REVERT: H 370 ASN cc_start: 0.8537 (t0) cc_final: 0.8225 (t0) REVERT: H 388 MET cc_start: 0.8392 (mtp) cc_final: 0.7995 (mmt) REVERT: H 390 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7863 (ttm110) REVERT: H 404 ASP cc_start: 0.8332 (p0) cc_final: 0.7600 (p0) REVERT: H 407 GLU cc_start: 0.8926 (tp30) cc_final: 0.8723 (mm-30) REVERT: H 426 GLN cc_start: 0.7806 (tt0) cc_final: 0.7536 (tp40) REVERT: I 121 ARG cc_start: 0.8841 (ttm110) cc_final: 0.8396 (mtm180) REVERT: I 123 GLU cc_start: 0.9452 (mm-30) cc_final: 0.8822 (mm-30) REVERT: I 279 GLN cc_start: 0.8645 (pt0) cc_final: 0.8119 (pt0) REVERT: I 299 MET cc_start: 0.8220 (mmm) cc_final: 0.7584 (mmm) REVERT: I 321 MET cc_start: 0.8650 (ptp) cc_final: 0.8359 (ptp) REVERT: I 351 VAL cc_start: 0.9242 (t) cc_final: 0.9019 (p) REVERT: I 375 GLN cc_start: 0.8278 (pp30) cc_final: 0.7848 (pp30) REVERT: B 8 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: B 50 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: B 66 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7908 (t) REVERT: B 73 MET cc_start: 0.8571 (mmm) cc_final: 0.8199 (mtt) REVERT: B 99 ASN cc_start: 0.8782 (t0) cc_final: 0.7972 (t0) REVERT: B 133 PHE cc_start: 0.8140 (m-80) cc_final: 0.7622 (m-80) REVERT: B 167 PHE cc_start: 0.8141 (m-10) cc_final: 0.7290 (m-10) REVERT: B 329 GLN cc_start: 0.8946 (mm110) cc_final: 0.8685 (tp40) REVERT: B 363 MET cc_start: 0.8504 (pmm) cc_final: 0.8185 (pmm) REVERT: B 370 ASN cc_start: 0.7991 (t0) cc_final: 0.7481 (t0) REVERT: B 405 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 406 MET cc_start: 0.8707 (tpp) cc_final: 0.7605 (tpp) REVERT: B 424 GLN cc_start: 0.8808 (tt0) cc_final: 0.8255 (tt0) outliers start: 277 outliers final: 193 residues processed: 1662 average time/residue: 0.2302 time to fit residues: 624.7552 Evaluate side-chains 1637 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1413 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 309 HIS Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 308 ARG Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 266 PHE Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 266 PHE Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 143 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 458 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 504 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN E 206 ASN E 256 GLN E 258 ASN ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 300 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS F 375 GLN D 307 HIS D 423 GLN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN H 337 ASN I 307 HIS ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 307 HIS B 337 ASN B 423 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.105720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.089102 restraints weight = 90810.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092340 restraints weight = 45216.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.094552 restraints weight = 27480.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.096093 restraints weight = 18898.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.097159 restraints weight = 14143.124| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41998 Z= 0.167 Angle : 0.686 14.306 57035 Z= 0.348 Chirality : 0.046 0.286 6240 Planarity : 0.005 0.048 7411 Dihedral : 10.129 137.570 5859 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 6.25 % Allowed : 25.45 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 5136 helix: 1.08 (0.10), residues: 2484 sheet: -0.70 (0.19), residues: 744 loop : -1.58 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 339 TYR 0.051 0.001 TYR C 210 PHE 0.048 0.002 PHE L 255 TRP 0.022 0.002 TRP B 344 HIS 0.027 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00374 (41998) covalent geometry : angle 0.68583 (57035) hydrogen bonds : bond 0.04490 ( 2184) hydrogen bonds : angle 4.97930 ( 6354) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1718 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 1442 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7778 (tm-30) REVERT: A 96 LYS cc_start: 0.8685 (tppt) cc_final: 0.8452 (tppp) REVERT: A 120 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8169 (t0) REVERT: A 121 ARG cc_start: 0.8350 (mmm160) cc_final: 0.7933 (tpt170) REVERT: A 169 PHE cc_start: 0.8750 (m-80) cc_final: 0.8521 (m-80) REVERT: A 224 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: A 254 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 256 GLN cc_start: 0.9368 (pt0) cc_final: 0.8702 (pm20) REVERT: A 309 HIS cc_start: 0.8019 (m90) cc_final: 0.7779 (m90) REVERT: A 327 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8743 (p0) REVERT: A 357 TYR cc_start: 0.8706 (m-80) cc_final: 0.8347 (m-80) REVERT: A 386 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7149 (pt0) REVERT: A 430 LYS cc_start: 0.9410 (ttmt) cc_final: 0.9135 (tptt) REVERT: C 90 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8193 (tp30) REVERT: C 145 THR cc_start: 0.7753 (m) cc_final: 0.7363 (m) REVERT: C 169 PHE cc_start: 0.8708 (m-80) cc_final: 0.8397 (m-80) REVERT: C 269 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8359 (pp) REVERT: C 327 ASP cc_start: 0.9285 (OUTLIER) cc_final: 0.8788 (p0) REVERT: C 399 TYR cc_start: 0.8981 (t80) cc_final: 0.8586 (t80) REVERT: C 417 GLU cc_start: 0.8672 (mp0) cc_final: 0.8285 (mp0) REVERT: E 88 HIS cc_start: 0.6647 (OUTLIER) cc_final: 0.4808 (t70) REVERT: E 90 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7956 (tp30) REVERT: E 156 ARG cc_start: 0.8818 (mmt90) cc_final: 0.8510 (mmm-85) REVERT: E 214 ARG cc_start: 0.8882 (tmm-80) cc_final: 0.8181 (tmm-80) REVERT: E 248 LEU cc_start: 0.9077 (tp) cc_final: 0.8794 (tt) REVERT: E 269 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8546 (pp) REVERT: E 327 ASP cc_start: 0.9195 (OUTLIER) cc_final: 0.8813 (p0) REVERT: E 408 TYR cc_start: 0.9228 (m-80) cc_final: 0.8986 (m-10) REVERT: E 430 LYS cc_start: 0.9550 (ttmt) cc_final: 0.9251 (tptt) REVERT: J 36 MET cc_start: 0.8397 (ttp) cc_final: 0.8096 (tmm) REVERT: J 76 ASP cc_start: 0.8834 (m-30) cc_final: 0.8609 (m-30) REVERT: J 88 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.5180 (t70) REVERT: J 90 GLU cc_start: 0.8311 (tp30) cc_final: 0.7929 (tp30) REVERT: J 108 TYR cc_start: 0.9085 (m-80) cc_final: 0.8672 (m-80) REVERT: J 244 PHE cc_start: 0.8783 (m-80) cc_final: 0.8300 (m-80) REVERT: J 308 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8171 (ptp90) REVERT: J 339 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7714 (ptm160) REVERT: J 346 TRP cc_start: 0.8550 (p-90) cc_final: 0.4529 (t-100) REVERT: J 413 MET cc_start: 0.8637 (tpp) cc_final: 0.8429 (mmm) REVERT: J 423 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8932 (mt-10) REVERT: J 430 LYS cc_start: 0.9597 (ttmt) cc_final: 0.9246 (tptt) REVERT: J 432 TYR cc_start: 0.8662 (m-80) cc_final: 0.7988 (t80) REVERT: K 3 GLU cc_start: 0.7610 (mp0) cc_final: 0.7177 (mp0) REVERT: K 6 SER cc_start: 0.8994 (m) cc_final: 0.8698 (t) REVERT: K 69 ASP cc_start: 0.8665 (t0) cc_final: 0.8328 (t0) REVERT: K 71 GLU cc_start: 0.8057 (tt0) cc_final: 0.7760 (tt0) REVERT: K 90 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7705 (tp30) REVERT: K 108 TYR cc_start: 0.9074 (m-80) cc_final: 0.8366 (m-10) REVERT: K 210 TYR cc_start: 0.8830 (m-10) cc_final: 0.8451 (m-80) REVERT: K 211 ASP cc_start: 0.9298 (m-30) cc_final: 0.9038 (m-30) REVERT: K 251 ASP cc_start: 0.7820 (t70) cc_final: 0.7522 (t70) REVERT: K 256 GLN cc_start: 0.9085 (pt0) cc_final: 0.8795 (tm-30) REVERT: K 287 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8185 (p) REVERT: K 300 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8803 (t0) REVERT: K 346 TRP cc_start: 0.8527 (p-90) cc_final: 0.4141 (t-100) REVERT: K 357 TYR cc_start: 0.8658 (m-80) cc_final: 0.8117 (m-80) REVERT: K 386 GLU cc_start: 0.8652 (tt0) cc_final: 0.8252 (pt0) REVERT: K 430 LYS cc_start: 0.9549 (ttmt) cc_final: 0.9102 (tptt) REVERT: K 432 TYR cc_start: 0.8622 (m-80) cc_final: 0.7887 (t80) REVERT: K 433 GLU cc_start: 0.9142 (tt0) cc_final: 0.8845 (tp30) REVERT: L 69 ASP cc_start: 0.8672 (t0) cc_final: 0.8406 (t0) REVERT: L 71 GLU cc_start: 0.8162 (tt0) cc_final: 0.7942 (tt0) REVERT: L 76 ASP cc_start: 0.8907 (m-30) cc_final: 0.8646 (m-30) REVERT: L 90 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: L 109 THR cc_start: 0.8631 (m) cc_final: 0.8224 (p) REVERT: L 210 TYR cc_start: 0.8834 (m-10) cc_final: 0.8525 (m-80) REVERT: L 224 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7971 (m-10) REVERT: L 232 SER cc_start: 0.9266 (m) cc_final: 0.8877 (p) REVERT: L 346 TRP cc_start: 0.8576 (p-90) cc_final: 0.4628 (t-100) REVERT: L 372 GLN cc_start: 0.8807 (mp10) cc_final: 0.8537 (pm20) REVERT: L 394 LYS cc_start: 0.9269 (mppt) cc_final: 0.8924 (mppt) REVERT: L 417 GLU cc_start: 0.7975 (mp0) cc_final: 0.7691 (mp0) REVERT: L 432 TYR cc_start: 0.8578 (m-80) cc_final: 0.7845 (t80) REVERT: F 14 ASN cc_start: 0.8753 (m-40) cc_final: 0.8395 (m-40) REVERT: F 122 LYS cc_start: 0.9141 (pttp) cc_final: 0.8900 (ptmm) REVERT: F 129 CYS cc_start: 0.7489 (t) cc_final: 0.7015 (p) REVERT: F 159 TYR cc_start: 0.8641 (m-80) cc_final: 0.8046 (m-80) REVERT: F 165 ASN cc_start: 0.9006 (m110) cc_final: 0.8774 (m110) REVERT: F 200 TYR cc_start: 0.8859 (m-80) cc_final: 0.8560 (m-80) REVERT: F 226 ASN cc_start: 0.9234 (m-40) cc_final: 0.8858 (m-40) REVERT: F 310 TYR cc_start: 0.9167 (m-80) cc_final: 0.8950 (m-80) REVERT: F 325 GLU cc_start: 0.8761 (tt0) cc_final: 0.8272 (pt0) REVERT: F 326 VAL cc_start: 0.9219 (t) cc_final: 0.8993 (p) REVERT: F 329 GLN cc_start: 0.9277 (tp40) cc_final: 0.8969 (tp40) REVERT: F 330 MET cc_start: 0.8822 (mmt) cc_final: 0.8517 (mmt) REVERT: F 375 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7800 (pp30) REVERT: F 405 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8184 (tm-30) REVERT: F 406 MET cc_start: 0.8638 (tpp) cc_final: 0.7686 (tpp) REVERT: F 410 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8593 (mt-10) REVERT: F 422 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8137 (t80) REVERT: D 22 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7829 (tm-30) REVERT: D 26 ASP cc_start: 0.8417 (m-30) cc_final: 0.7943 (m-30) REVERT: D 99 ASN cc_start: 0.8448 (t0) cc_final: 0.8083 (t0) REVERT: D 122 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.9037 (tppt) REVERT: D 156 ARG cc_start: 0.7909 (tpp-160) cc_final: 0.7192 (tpp-160) REVERT: D 159 TYR cc_start: 0.8526 (m-80) cc_final: 0.8065 (m-10) REVERT: D 164 MET cc_start: 0.8835 (mmm) cc_final: 0.8284 (mtt) REVERT: D 194 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8341 (mm-30) REVERT: D 213 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8109 (ttp-110) REVERT: D 279 GLN cc_start: 0.8733 (pt0) cc_final: 0.8269 (pt0) REVERT: D 323 MET cc_start: 0.8235 (mpp) cc_final: 0.7669 (mpp) REVERT: D 344 TRP cc_start: 0.8983 (OUTLIER) cc_final: 0.8014 (p-90) REVERT: D 375 GLN cc_start: 0.8446 (pp30) cc_final: 0.6835 (pp30) REVERT: D 376 GLU cc_start: 0.8779 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 379 LYS cc_start: 0.9438 (mtpt) cc_final: 0.8992 (ptpt) REVERT: D 405 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8163 (tm-30) REVERT: D 422 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8083 (t80) REVERT: G 14 ASN cc_start: 0.8849 (m-40) cc_final: 0.8619 (m-40) REVERT: G 31 ASP cc_start: 0.8860 (m-30) cc_final: 0.8514 (m-30) REVERT: G 50 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: G 121 ARG cc_start: 0.8887 (ttm110) cc_final: 0.8440 (mtm180) REVERT: G 143 THR cc_start: 0.8506 (m) cc_final: 0.8277 (m) REVERT: G 156 ARG cc_start: 0.8305 (ttt180) cc_final: 0.8064 (ttt180) REVERT: G 213 ARG cc_start: 0.8312 (ttp-110) cc_final: 0.8102 (ttp-110) REVERT: G 226 ASN cc_start: 0.8940 (m-40) cc_final: 0.8669 (m-40) REVERT: G 237 THR cc_start: 0.8677 (m) cc_final: 0.8442 (m) REVERT: G 276 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7883 (mmm160) REVERT: G 291 GLN cc_start: 0.8814 (mp10) cc_final: 0.8499 (mp10) REVERT: G 310 TYR cc_start: 0.9128 (m-10) cc_final: 0.8861 (m-80) REVERT: G 375 GLN cc_start: 0.8353 (pp30) cc_final: 0.7927 (pp30) REVERT: H 50 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: H 67 ASP cc_start: 0.8316 (t0) cc_final: 0.8099 (t70) REVERT: H 73 MET cc_start: 0.8700 (mmm) cc_final: 0.8368 (mtm) REVERT: H 111 GLU cc_start: 0.8872 (mp0) cc_final: 0.8593 (mp0) REVERT: H 195 ASN cc_start: 0.9145 (m-40) cc_final: 0.8903 (m-40) REVERT: H 208 TYR cc_start: 0.8977 (m-10) cc_final: 0.8503 (m-80) REVERT: H 329 GLN cc_start: 0.9170 (mm110) cc_final: 0.8599 (mm-40) REVERT: H 337 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7277 (t0) REVERT: H 344 TRP cc_start: 0.9129 (OUTLIER) cc_final: 0.8360 (p-90) REVERT: H 370 ASN cc_start: 0.8555 (t0) cc_final: 0.8172 (t0) REVERT: H 375 GLN cc_start: 0.8357 (pp30) cc_final: 0.7888 (pp30) REVERT: H 376 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8223 (mt-10) REVERT: H 390 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7858 (ttm110) REVERT: H 426 GLN cc_start: 0.7791 (tt0) cc_final: 0.7474 (tm-30) REVERT: I 121 ARG cc_start: 0.8846 (ttm110) cc_final: 0.8412 (mtm180) REVERT: I 123 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8808 (mm-30) REVERT: I 279 GLN cc_start: 0.8678 (pt0) cc_final: 0.8148 (pt0) REVERT: I 299 MET cc_start: 0.8092 (mmm) cc_final: 0.7789 (mmm) REVERT: I 375 GLN cc_start: 0.8259 (pp30) cc_final: 0.7800 (pp30) REVERT: B 73 MET cc_start: 0.8565 (mmm) cc_final: 0.8169 (mtt) REVERT: B 99 ASN cc_start: 0.8779 (t0) cc_final: 0.8165 (t0) REVERT: B 122 LYS cc_start: 0.9121 (pttp) cc_final: 0.8811 (ptmm) REVERT: B 133 PHE cc_start: 0.8024 (m-80) cc_final: 0.7492 (m-80) REVERT: B 328 GLU cc_start: 0.8595 (pp20) cc_final: 0.8284 (pp20) REVERT: B 329 GLN cc_start: 0.8968 (mm110) cc_final: 0.8572 (tp40) REVERT: B 363 MET cc_start: 0.8521 (pmm) cc_final: 0.8270 (pmm) REVERT: B 405 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8056 (tm-30) REVERT: B 406 MET cc_start: 0.8720 (tpp) cc_final: 0.7650 (tpp) REVERT: B 424 GLN cc_start: 0.8818 (tt0) cc_final: 0.8314 (tt0) outliers start: 276 outliers final: 212 residues processed: 1591 average time/residue: 0.2275 time to fit residues: 596.0602 Evaluate side-chains 1628 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 1388 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 308 ARG Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 376 CYS Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 398 MET Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 375 GLN Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 266 PHE Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 266 PHE Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 178 optimal weight: 7.9990 chunk 375 optimal weight: 9.9990 chunk 373 optimal weight: 2.9990 chunk 264 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 454 optimal weight: 5.9990 chunk 267 optimal weight: 0.0970 chunk 391 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 285 GLN E 101 ASN E 256 GLN ** J 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS F 375 GLN D 307 HIS D 423 GLN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN H 337 ASN H 375 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 ASN I 307 HIS ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 ASN B 227 HIS ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 423 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.106178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089508 restraints weight = 91095.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.092764 restraints weight = 45443.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.094995 restraints weight = 27650.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096540 restraints weight = 18926.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097617 restraints weight = 14166.691| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 41998 Z= 0.163 Angle : 0.695 14.377 57035 Z= 0.352 Chirality : 0.046 0.292 6240 Planarity : 0.005 0.047 7411 Dihedral : 10.062 136.482 5857 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 6.34 % Allowed : 26.35 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 5136 helix: 0.99 (0.10), residues: 2520 sheet: -0.64 (0.19), residues: 744 loop : -1.71 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 390 TYR 0.052 0.001 TYR C 210 PHE 0.048 0.002 PHE L 255 TRP 0.019 0.002 TRP B 344 HIS 0.012 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00369 (41998) covalent geometry : angle 0.69517 (57035) hydrogen bonds : bond 0.04464 ( 2184) hydrogen bonds : angle 4.94604 ( 6354) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1741 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 1461 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7779 (tm-30) REVERT: A 96 LYS cc_start: 0.8736 (tppt) cc_final: 0.8378 (tppp) REVERT: A 120 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8146 (t0) REVERT: A 121 ARG cc_start: 0.8330 (mmm160) cc_final: 0.7919 (tpt170) REVERT: A 153 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9326 (mp) REVERT: A 224 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: A 254 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: A 256 GLN cc_start: 0.9378 (pt0) cc_final: 0.8711 (pm20) REVERT: A 357 TYR cc_start: 0.8632 (m-80) cc_final: 0.8251 (m-80) REVERT: A 386 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: A 430 LYS cc_start: 0.9416 (ttmt) cc_final: 0.9140 (tptt) REVERT: C 90 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8243 (tp30) REVERT: C 123 ARG cc_start: 0.8808 (ttm170) cc_final: 0.8590 (tpp80) REVERT: C 145 THR cc_start: 0.7731 (m) cc_final: 0.7400 (m) REVERT: C 169 PHE cc_start: 0.8694 (m-80) cc_final: 0.8394 (m-80) REVERT: C 269 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8372 (pp) REVERT: C 399 TYR cc_start: 0.8995 (t80) cc_final: 0.8607 (t80) REVERT: C 417 GLU cc_start: 0.8670 (mp0) cc_final: 0.8327 (mp0) REVERT: E 88 HIS cc_start: 0.6525 (OUTLIER) cc_final: 0.4660 (t70) REVERT: E 90 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7956 (tp30) REVERT: E 206 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8198 (m-40) REVERT: E 248 LEU cc_start: 0.9100 (tp) cc_final: 0.8795 (tt) REVERT: E 249 ASN cc_start: 0.8660 (m-40) cc_final: 0.8310 (m-40) REVERT: E 269 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8479 (pp) REVERT: E 372 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: E 408 TYR cc_start: 0.9282 (m-80) cc_final: 0.9015 (m-80) REVERT: E 430 LYS cc_start: 0.9553 (ttmt) cc_final: 0.9258 (tptt) REVERT: J 36 MET cc_start: 0.8408 (ttp) cc_final: 0.8121 (tmm) REVERT: J 76 ASP cc_start: 0.8815 (m-30) cc_final: 0.8583 (m-30) REVERT: J 88 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.5181 (t70) REVERT: J 90 GLU cc_start: 0.8328 (tp30) cc_final: 0.7948 (tp30) REVERT: J 103 TYR cc_start: 0.8796 (t80) cc_final: 0.8524 (t80) REVERT: J 108 TYR cc_start: 0.9075 (m-80) cc_final: 0.8655 (m-80) REVERT: J 262 TYR cc_start: 0.8760 (m-80) cc_final: 0.8554 (m-80) REVERT: J 308 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8178 (ptp90) REVERT: J 327 ASP cc_start: 0.9360 (OUTLIER) cc_final: 0.9153 (p0) REVERT: J 339 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7638 (ptm160) REVERT: J 346 TRP cc_start: 0.8573 (p-90) cc_final: 0.4478 (t-100) REVERT: J 413 MET cc_start: 0.8647 (tpp) cc_final: 0.8430 (mmm) REVERT: J 423 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8939 (mt-10) REVERT: J 430 LYS cc_start: 0.9593 (ttmt) cc_final: 0.9239 (tptt) REVERT: J 432 TYR cc_start: 0.8635 (m-80) cc_final: 0.7980 (t80) REVERT: K 6 SER cc_start: 0.8920 (m) cc_final: 0.8663 (t) REVERT: K 69 ASP cc_start: 0.8606 (t0) cc_final: 0.8351 (t0) REVERT: K 71 GLU cc_start: 0.8126 (tt0) cc_final: 0.7729 (tt0) REVERT: K 90 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: K 108 TYR cc_start: 0.9018 (m-80) cc_final: 0.8319 (m-10) REVERT: K 154 MET cc_start: 0.8780 (mmm) cc_final: 0.8474 (mmm) REVERT: K 211 ASP cc_start: 0.9288 (m-30) cc_final: 0.9019 (m-30) REVERT: K 251 ASP cc_start: 0.7762 (t70) cc_final: 0.7536 (t70) REVERT: K 256 GLN cc_start: 0.9087 (pt0) cc_final: 0.8714 (tm-30) REVERT: K 287 SER cc_start: 0.8427 (OUTLIER) cc_final: 0.8152 (p) REVERT: K 300 ASN cc_start: 0.8992 (t0) cc_final: 0.8782 (t0) REVERT: K 346 TRP cc_start: 0.8551 (p-90) cc_final: 0.4225 (t-100) REVERT: K 357 TYR cc_start: 0.8641 (m-80) cc_final: 0.8095 (m-80) REVERT: K 386 GLU cc_start: 0.8613 (tt0) cc_final: 0.8251 (pt0) REVERT: K 430 LYS cc_start: 0.9558 (ttmt) cc_final: 0.9128 (tptt) REVERT: K 432 TYR cc_start: 0.8611 (m-80) cc_final: 0.7871 (t80) REVERT: K 433 GLU cc_start: 0.9122 (tt0) cc_final: 0.8836 (tp30) REVERT: L 6 SER cc_start: 0.8971 (m) cc_final: 0.8705 (t) REVERT: L 69 ASP cc_start: 0.8683 (t0) cc_final: 0.8331 (t70) REVERT: L 71 GLU cc_start: 0.8175 (tt0) cc_final: 0.7971 (tt0) REVERT: L 76 ASP cc_start: 0.8902 (m-30) cc_final: 0.8650 (m-30) REVERT: L 90 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: L 109 THR cc_start: 0.8660 (m) cc_final: 0.8277 (p) REVERT: L 210 TYR cc_start: 0.8791 (m-10) cc_final: 0.8561 (m-80) REVERT: L 232 SER cc_start: 0.9247 (m) cc_final: 0.8876 (p) REVERT: L 342 GLN cc_start: 0.7962 (pm20) cc_final: 0.7727 (pm20) REVERT: L 346 TRP cc_start: 0.8467 (p-90) cc_final: 0.4619 (t-100) REVERT: L 352 LYS cc_start: 0.2437 (mptt) cc_final: 0.2164 (mptt) REVERT: L 372 GLN cc_start: 0.8844 (mp10) cc_final: 0.8580 (pm20) REVERT: L 394 LYS cc_start: 0.9296 (mppt) cc_final: 0.8935 (mppt) REVERT: L 413 MET cc_start: 0.8717 (mmm) cc_final: 0.8481 (tpp) REVERT: L 432 TYR cc_start: 0.8578 (m-80) cc_final: 0.7852 (t80) REVERT: F 14 ASN cc_start: 0.8715 (m-40) cc_final: 0.8412 (m-40) REVERT: F 122 LYS cc_start: 0.9142 (pttp) cc_final: 0.8908 (ptmm) REVERT: F 129 CYS cc_start: 0.7414 (t) cc_final: 0.6818 (p) REVERT: F 130 LEU cc_start: 0.8790 (tp) cc_final: 0.8488 (tp) REVERT: F 159 TYR cc_start: 0.8614 (m-80) cc_final: 0.8050 (m-80) REVERT: F 162 ARG cc_start: 0.8698 (mmt-90) cc_final: 0.8417 (mmp80) REVERT: F 165 ASN cc_start: 0.9068 (m110) cc_final: 0.8791 (m110) REVERT: F 213 ARG cc_start: 0.8547 (ttm110) cc_final: 0.8321 (ptp-110) REVERT: F 226 ASN cc_start: 0.9189 (m-40) cc_final: 0.8832 (m-40) REVERT: F 245 GLN cc_start: 0.8620 (mp10) cc_final: 0.8362 (mp10) REVERT: F 325 GLU cc_start: 0.8757 (tt0) cc_final: 0.8554 (pt0) REVERT: F 330 MET cc_start: 0.8800 (mmt) cc_final: 0.8457 (mmt) REVERT: F 333 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9167 (tp) REVERT: F 375 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7960 (pp30) REVERT: F 379 LYS cc_start: 0.9488 (ptmt) cc_final: 0.9137 (pttp) REVERT: F 405 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8088 (tm-30) REVERT: F 422 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8178 (t80) REVERT: F 424 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: D 22 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7790 (tm-30) REVERT: D 26 ASP cc_start: 0.8389 (m-30) cc_final: 0.7909 (m-30) REVERT: D 58 LYS cc_start: 0.8240 (mmtm) cc_final: 0.7778 (mmtp) REVERT: D 86 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8469 (ttp80) REVERT: D 99 ASN cc_start: 0.8432 (t0) cc_final: 0.8034 (t0) REVERT: D 194 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8365 (mm-30) REVERT: D 213 ARG cc_start: 0.8487 (ttp-110) cc_final: 0.8092 (ttp-110) REVERT: D 289 LEU cc_start: 0.9445 (mt) cc_final: 0.9195 (mp) REVERT: D 323 MET cc_start: 0.8302 (mpp) cc_final: 0.7429 (mpp) REVERT: D 328 GLU cc_start: 0.8798 (pp20) cc_final: 0.8511 (pp20) REVERT: D 329 GLN cc_start: 0.9140 (tp40) cc_final: 0.8787 (tp40) REVERT: D 344 TRP cc_start: 0.9004 (OUTLIER) cc_final: 0.8010 (p-90) REVERT: D 363 MET cc_start: 0.8606 (pmm) cc_final: 0.8202 (pmm) REVERT: D 375 GLN cc_start: 0.8412 (pp30) cc_final: 0.7124 (pp30) REVERT: D 376 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8210 (mt-10) REVERT: D 379 LYS cc_start: 0.9436 (mtpt) cc_final: 0.8742 (mtpt) REVERT: D 392 LYS cc_start: 0.9183 (mmtp) cc_final: 0.8929 (mmtt) REVERT: D 405 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8124 (tm-30) REVERT: D 422 TYR cc_start: 0.9069 (OUTLIER) cc_final: 0.8085 (t80) REVERT: G 14 ASN cc_start: 0.8831 (m-40) cc_final: 0.8597 (m-40) REVERT: G 31 ASP cc_start: 0.8864 (m-30) cc_final: 0.8511 (m-30) REVERT: G 50 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: G 121 ARG cc_start: 0.8872 (ttm110) cc_final: 0.8424 (mtm180) REVERT: G 156 ARG cc_start: 0.8299 (ttt180) cc_final: 0.8050 (ttt180) REVERT: G 209 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8209 (p0) REVERT: G 226 ASN cc_start: 0.8932 (m-40) cc_final: 0.8660 (m-40) REVERT: G 276 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7909 (mmm160) REVERT: G 291 GLN cc_start: 0.8827 (mp10) cc_final: 0.8461 (mp10) REVERT: G 297 LYS cc_start: 0.8931 (tppt) cc_final: 0.8090 (tppt) REVERT: G 310 TYR cc_start: 0.9138 (m-10) cc_final: 0.8905 (m-80) REVERT: H 50 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: H 73 MET cc_start: 0.8672 (mmm) cc_final: 0.8369 (mtm) REVERT: H 111 GLU cc_start: 0.8886 (mp0) cc_final: 0.8612 (mp0) REVERT: H 195 ASN cc_start: 0.9131 (m-40) cc_final: 0.8886 (m-40) REVERT: H 208 TYR cc_start: 0.8942 (m-10) cc_final: 0.8616 (m-80) REVERT: H 337 ASN cc_start: 0.7641 (OUTLIER) cc_final: 0.7315 (t0) REVERT: H 344 TRP cc_start: 0.9119 (OUTLIER) cc_final: 0.8262 (p-90) REVERT: H 370 ASN cc_start: 0.8510 (t0) cc_final: 0.8149 (t0) REVERT: H 388 MET cc_start: 0.8399 (mtp) cc_final: 0.7996 (mmt) REVERT: H 390 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7876 (ttm110) REVERT: H 426 GLN cc_start: 0.7756 (tt0) cc_final: 0.7425 (tm-30) REVERT: I 121 ARG cc_start: 0.8871 (ttm110) cc_final: 0.8422 (mtm180) REVERT: I 123 GLU cc_start: 0.9435 (mm-30) cc_final: 0.8772 (mm-30) REVERT: I 279 GLN cc_start: 0.8690 (pt0) cc_final: 0.8145 (pt0) REVERT: I 291 GLN cc_start: 0.8715 (mt0) cc_final: 0.8280 (mp10) REVERT: I 299 MET cc_start: 0.8090 (mmm) cc_final: 0.7860 (mmm) REVERT: I 321 MET cc_start: 0.8686 (ptp) cc_final: 0.8352 (ptp) REVERT: I 375 GLN cc_start: 0.8287 (pp30) cc_final: 0.7765 (pp30) REVERT: I 426 GLN cc_start: 0.8002 (tt0) cc_final: 0.7751 (tm-30) REVERT: B 122 LYS cc_start: 0.9090 (pttp) cc_final: 0.8811 (ptmm) REVERT: B 133 PHE cc_start: 0.7967 (m-80) cc_final: 0.7450 (m-80) REVERT: B 328 GLU cc_start: 0.8651 (pp20) cc_final: 0.8333 (pp20) REVERT: B 329 GLN cc_start: 0.8986 (mm110) cc_final: 0.8577 (tp40) REVERT: B 363 MET cc_start: 0.8497 (pmm) cc_final: 0.8245 (pmm) REVERT: B 405 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 406 MET cc_start: 0.8719 (tpp) cc_final: 0.7691 (tpp) outliers start: 280 outliers final: 204 residues processed: 1619 average time/residue: 0.2279 time to fit residues: 606.6943 Evaluate side-chains 1659 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1427 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 308 ARG Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 GLU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 375 GLN Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 266 PHE Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 266 PHE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 266 PHE Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 325 GLU Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 460 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 312 optimal weight: 8.9990 chunk 370 optimal weight: 0.2980 chunk 164 optimal weight: 8.9990 chunk 381 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 178 optimal weight: 6.9990 chunk 194 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 47 optimal weight: 10.0000 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 128 GLN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 GLN E 206 ASN E 256 GLN J 107 HIS ** J 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 300 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 GLN ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 426 GLN D 11 GLN D 307 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.089787 restraints weight = 90517.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.093015 restraints weight = 45564.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.095224 restraints weight = 27828.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.096774 restraints weight = 19165.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.097880 restraints weight = 14319.786| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 41998 Z= 0.158 Angle : 0.714 14.161 57035 Z= 0.361 Chirality : 0.046 0.262 6240 Planarity : 0.005 0.051 7411 Dihedral : 9.898 139.349 5845 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 5.68 % Allowed : 27.28 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.12), residues: 5136 helix: 1.04 (0.10), residues: 2490 sheet: -0.55 (0.19), residues: 744 loop : -1.56 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 339 TYR 0.054 0.001 TYR C 210 PHE 0.048 0.002 PHE L 255 TRP 0.018 0.001 TRP B 344 HIS 0.011 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00359 (41998) covalent geometry : angle 0.71418 (57035) hydrogen bonds : bond 0.04437 ( 2184) hydrogen bonds : angle 4.93546 ( 6354) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1708 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 1457 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7802 (tp30) REVERT: A 96 LYS cc_start: 0.8664 (tppt) cc_final: 0.8452 (tppp) REVERT: A 120 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8183 (t0) REVERT: A 121 ARG cc_start: 0.8377 (mmm160) cc_final: 0.7987 (tpt170) REVERT: A 153 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9321 (mp) REVERT: A 221 ARG cc_start: 0.7681 (mmt90) cc_final: 0.7473 (mmm-85) REVERT: A 224 TYR cc_start: 0.8267 (OUTLIER) cc_final: 0.7927 (m-80) REVERT: A 256 GLN cc_start: 0.9363 (pt0) cc_final: 0.8705 (pm20) REVERT: A 357 TYR cc_start: 0.8586 (m-80) cc_final: 0.8240 (m-80) REVERT: A 386 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: A 430 LYS cc_start: 0.9404 (ttmt) cc_final: 0.9161 (tptt) REVERT: C 90 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8000 (tm-30) REVERT: C 123 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8581 (tpp80) REVERT: C 169 PHE cc_start: 0.8672 (m-80) cc_final: 0.8404 (m-80) REVERT: C 269 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8385 (pp) REVERT: C 399 TYR cc_start: 0.8952 (t80) cc_final: 0.8659 (t80) REVERT: C 417 GLU cc_start: 0.8626 (mp0) cc_final: 0.8326 (mp0) REVERT: E 88 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.4706 (t70) REVERT: E 90 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7919 (tp30) REVERT: E 248 LEU cc_start: 0.9114 (tp) cc_final: 0.8823 (tt) REVERT: E 249 ASN cc_start: 0.8613 (m-40) cc_final: 0.8290 (m-40) REVERT: E 269 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8474 (pp) REVERT: E 372 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8040 (mp10) REVERT: E 430 LYS cc_start: 0.9544 (ttmt) cc_final: 0.9252 (tptt) REVERT: J 36 MET cc_start: 0.8464 (ttp) cc_final: 0.8177 (tmm) REVERT: J 76 ASP cc_start: 0.8811 (m-30) cc_final: 0.8559 (m-30) REVERT: J 88 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.5272 (t70) REVERT: J 90 GLU cc_start: 0.8327 (tp30) cc_final: 0.8078 (tp30) REVERT: J 108 TYR cc_start: 0.9079 (m-80) cc_final: 0.8586 (m-80) REVERT: J 206 ASN cc_start: 0.8567 (m110) cc_final: 0.8326 (m-40) REVERT: J 210 TYR cc_start: 0.8871 (m-10) cc_final: 0.8655 (m-80) REVERT: J 327 ASP cc_start: 0.9351 (OUTLIER) cc_final: 0.8956 (p0) REVERT: J 339 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7607 (ptm160) REVERT: J 346 TRP cc_start: 0.8592 (p-90) cc_final: 0.4582 (t-100) REVERT: J 413 MET cc_start: 0.8651 (tpp) cc_final: 0.8434 (mmm) REVERT: J 430 LYS cc_start: 0.9587 (ttmt) cc_final: 0.9231 (tptt) REVERT: J 432 TYR cc_start: 0.8607 (m-80) cc_final: 0.7977 (t80) REVERT: K 6 SER cc_start: 0.9004 (m) cc_final: 0.8732 (t) REVERT: K 69 ASP cc_start: 0.8582 (t0) cc_final: 0.8353 (t0) REVERT: K 71 GLU cc_start: 0.8160 (tt0) cc_final: 0.7789 (tt0) REVERT: K 90 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7653 (tp30) REVERT: K 112 LYS cc_start: 0.9000 (mttt) cc_final: 0.8712 (mmtm) REVERT: K 154 MET cc_start: 0.8774 (mmm) cc_final: 0.8497 (mmm) REVERT: K 211 ASP cc_start: 0.9301 (m-30) cc_final: 0.9048 (m-30) REVERT: K 256 GLN cc_start: 0.9097 (pt0) cc_final: 0.8720 (tm-30) REVERT: K 287 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8156 (p) REVERT: K 300 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8771 (t0) REVERT: K 346 TRP cc_start: 0.8553 (p-90) cc_final: 0.4268 (t-100) REVERT: K 357 TYR cc_start: 0.8629 (m-80) cc_final: 0.8099 (m-80) REVERT: K 386 GLU cc_start: 0.8620 (tt0) cc_final: 0.8188 (pt0) REVERT: K 408 TYR cc_start: 0.8839 (m-80) cc_final: 0.8142 (m-80) REVERT: K 430 LYS cc_start: 0.9555 (ttmt) cc_final: 0.9131 (tptt) REVERT: K 432 TYR cc_start: 0.8611 (m-80) cc_final: 0.7878 (t80) REVERT: K 433 GLU cc_start: 0.9109 (tt0) cc_final: 0.8824 (tp30) REVERT: L 6 SER cc_start: 0.8945 (m) cc_final: 0.8712 (t) REVERT: L 69 ASP cc_start: 0.8689 (t0) cc_final: 0.8241 (t70) REVERT: L 76 ASP cc_start: 0.8886 (m-30) cc_final: 0.8642 (m-30) REVERT: L 90 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: L 109 THR cc_start: 0.8618 (m) cc_final: 0.8252 (p) REVERT: L 113 GLU cc_start: 0.8897 (mp0) cc_final: 0.8667 (mp0) REVERT: L 145 THR cc_start: 0.7192 (m) cc_final: 0.6807 (m) REVERT: L 210 TYR cc_start: 0.8864 (m-10) cc_final: 0.8508 (m-80) REVERT: L 232 SER cc_start: 0.9242 (m) cc_final: 0.8874 (p) REVERT: L 346 TRP cc_start: 0.8408 (p-90) cc_final: 0.4609 (t-100) REVERT: L 372 GLN cc_start: 0.8857 (mp10) cc_final: 0.8615 (pm20) REVERT: L 394 LYS cc_start: 0.9315 (mppt) cc_final: 0.8951 (mppt) REVERT: L 432 TYR cc_start: 0.8568 (m-80) cc_final: 0.7901 (t80) REVERT: F 14 ASN cc_start: 0.8678 (m-40) cc_final: 0.8390 (m-40) REVERT: F 129 CYS cc_start: 0.7330 (t) cc_final: 0.6752 (p) REVERT: F 156 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.7340 (tpp-160) REVERT: F 159 TYR cc_start: 0.8585 (m-80) cc_final: 0.7207 (m-80) REVERT: F 162 ARG cc_start: 0.8706 (mmt-90) cc_final: 0.8504 (mmp80) REVERT: F 198 GLU cc_start: 0.8828 (pt0) cc_final: 0.8549 (pt0) REVERT: F 213 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8110 (ptp-110) REVERT: F 226 ASN cc_start: 0.9182 (m-40) cc_final: 0.8825 (m-40) REVERT: F 245 GLN cc_start: 0.8605 (mp10) cc_final: 0.8313 (mp10) REVERT: F 286 VAL cc_start: 0.8723 (t) cc_final: 0.8251 (t) REVERT: F 297 LYS cc_start: 0.9092 (tttm) cc_final: 0.8889 (tttt) REVERT: F 310 TYR cc_start: 0.9119 (m-80) cc_final: 0.8795 (m-80) REVERT: F 325 GLU cc_start: 0.8782 (tt0) cc_final: 0.8240 (pt0) REVERT: F 330 MET cc_start: 0.8763 (mmt) cc_final: 0.8430 (mmt) REVERT: F 333 ILE cc_start: 0.9448 (OUTLIER) cc_final: 0.9170 (tp) REVERT: F 375 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7986 (pp30) REVERT: F 405 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8200 (tm-30) REVERT: F 424 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: D 22 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7811 (tm-30) REVERT: D 26 ASP cc_start: 0.8400 (m-30) cc_final: 0.7905 (m-30) REVERT: D 41 ASP cc_start: 0.8517 (p0) cc_final: 0.8311 (p0) REVERT: D 58 LYS cc_start: 0.8267 (mmtm) cc_final: 0.7795 (mmtp) REVERT: D 86 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8412 (ttp80) REVERT: D 103 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8396 (ttmt) REVERT: D 156 ARG cc_start: 0.7947 (tpp-160) cc_final: 0.6860 (tpp-160) REVERT: D 164 MET cc_start: 0.8938 (mmm) cc_final: 0.8163 (mtt) REVERT: D 213 ARG cc_start: 0.8452 (ttp-110) cc_final: 0.8022 (ttp-110) REVERT: D 328 GLU cc_start: 0.8795 (pp20) cc_final: 0.8431 (pp20) REVERT: D 329 GLN cc_start: 0.9157 (tp40) cc_final: 0.8831 (tp40) REVERT: D 344 TRP cc_start: 0.8999 (OUTLIER) cc_final: 0.8018 (p-90) REVERT: D 363 MET cc_start: 0.8543 (pmm) cc_final: 0.8084 (pmm) REVERT: D 375 GLN cc_start: 0.8464 (pp30) cc_final: 0.7257 (pp30) REVERT: D 376 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8174 (mt-10) REVERT: D 379 LYS cc_start: 0.9439 (mtpt) cc_final: 0.8762 (mtpt) REVERT: D 392 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8958 (mmtt) REVERT: D 404 ASP cc_start: 0.8733 (p0) cc_final: 0.8276 (p0) REVERT: D 410 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8508 (mt-10) REVERT: D 422 TYR cc_start: 0.9064 (OUTLIER) cc_final: 0.8166 (t80) REVERT: G 14 ASN cc_start: 0.8807 (m-40) cc_final: 0.8589 (m-40) REVERT: G 31 ASP cc_start: 0.8861 (m-30) cc_final: 0.8514 (m-30) REVERT: G 50 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: G 121 ARG cc_start: 0.8864 (ttm110) cc_final: 0.8438 (mtm180) REVERT: G 156 ARG cc_start: 0.8274 (ttt180) cc_final: 0.8041 (ttt180) REVERT: G 209 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8822 (p0) REVERT: G 213 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7909 (ptp90) REVERT: G 226 ASN cc_start: 0.8940 (m-40) cc_final: 0.8662 (m-40) REVERT: G 276 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7882 (mmm160) REVERT: G 291 GLN cc_start: 0.8727 (mp10) cc_final: 0.8422 (mp10) REVERT: G 310 TYR cc_start: 0.9162 (m-10) cc_final: 0.8901 (m-80) REVERT: G 375 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7939 (pp30) REVERT: H 50 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: H 73 MET cc_start: 0.8650 (mmm) cc_final: 0.8290 (mtm) REVERT: H 77 ARG cc_start: 0.9211 (ttm170) cc_final: 0.8939 (ttm110) REVERT: H 111 GLU cc_start: 0.8895 (mp0) cc_final: 0.8630 (mp0) REVERT: H 195 ASN cc_start: 0.9115 (m-40) cc_final: 0.8869 (m-40) REVERT: H 208 TYR cc_start: 0.8936 (m-10) cc_final: 0.8601 (m-80) REVERT: H 291 GLN cc_start: 0.8761 (mp10) cc_final: 0.8470 (mp10) REVERT: H 344 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8264 (p-90) REVERT: H 370 ASN cc_start: 0.8439 (t0) cc_final: 0.8090 (t0) REVERT: H 375 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7599 (pp30) REVERT: H 390 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7857 (ttm110) REVERT: H 426 GLN cc_start: 0.7716 (tt0) cc_final: 0.7416 (tm-30) REVERT: I 121 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8507 (mtm180) REVERT: I 279 GLN cc_start: 0.8640 (pt0) cc_final: 0.8127 (pt0) REVERT: I 321 MET cc_start: 0.8638 (ptp) cc_final: 0.8318 (ptp) REVERT: I 351 VAL cc_start: 0.9256 (t) cc_final: 0.9013 (p) REVERT: I 375 GLN cc_start: 0.8267 (pp30) cc_final: 0.6158 (pp30) REVERT: I 379 LYS cc_start: 0.9546 (ttmt) cc_final: 0.8877 (mtmm) REVERT: I 407 GLU cc_start: 0.8994 (tp30) cc_final: 0.8687 (tt0) REVERT: B 122 LYS cc_start: 0.9080 (pttp) cc_final: 0.8838 (ptmm) REVERT: B 133 PHE cc_start: 0.7950 (m-80) cc_final: 0.7427 (m-80) REVERT: B 162 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.8017 (tpp-160) REVERT: B 329 GLN cc_start: 0.8988 (mm110) cc_final: 0.8662 (tp40) REVERT: B 363 MET cc_start: 0.8502 (pmm) cc_final: 0.8233 (pmm) REVERT: B 405 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8049 (tm-30) REVERT: B 406 MET cc_start: 0.8739 (tpp) cc_final: 0.7704 (tpp) outliers start: 251 outliers final: 201 residues processed: 1592 average time/residue: 0.2234 time to fit residues: 587.2477 Evaluate side-chains 1634 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1407 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 372 GLN Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 375 GLN Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 266 PHE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 266 PHE Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 119 optimal weight: 0.6980 chunk 275 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 509 optimal weight: 9.9990 chunk 312 optimal weight: 9.9990 chunk 491 optimal weight: 5.9990 chunk 484 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 375 optimal weight: 0.0670 chunk 127 optimal weight: 3.9990 overall best weight: 3.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 285 GLN E 256 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN K 300 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 307 HIS ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 GLN ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS D 423 GLN G 329 GLN G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 337 ASN H 375 GLN ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 423 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.106495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.089890 restraints weight = 90552.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.093094 restraints weight = 45448.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.095295 restraints weight = 27799.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.096856 restraints weight = 19161.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.097908 restraints weight = 14307.072| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 41998 Z= 0.165 Angle : 0.736 14.374 57035 Z= 0.371 Chirality : 0.047 0.277 6240 Planarity : 0.005 0.054 7411 Dihedral : 9.896 139.395 5845 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 5.32 % Allowed : 28.05 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.12), residues: 5136 helix: 1.07 (0.10), residues: 2478 sheet: -0.50 (0.20), residues: 744 loop : -1.56 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 339 TYR 0.061 0.001 TYR E 210 PHE 0.048 0.002 PHE L 255 TRP 0.018 0.001 TRP B 344 HIS 0.011 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00377 (41998) covalent geometry : angle 0.73561 (57035) hydrogen bonds : bond 0.04432 ( 2184) hydrogen bonds : angle 4.96422 ( 6354) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10272 Ramachandran restraints generated. 5136 Oldfield, 0 Emsley, 5136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1687 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 1452 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7706 (tm-30) REVERT: A 96 LYS cc_start: 0.8623 (tppt) cc_final: 0.8401 (tppp) REVERT: A 120 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8201 (t0) REVERT: A 121 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8053 (tpt170) REVERT: A 128 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 153 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9324 (mp) REVERT: A 224 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7909 (m-80) REVERT: A 256 GLN cc_start: 0.9386 (pt0) cc_final: 0.8714 (pm20) REVERT: A 357 TYR cc_start: 0.8626 (m-80) cc_final: 0.8265 (m-80) REVERT: A 430 LYS cc_start: 0.9393 (ttmt) cc_final: 0.9156 (tptt) REVERT: C 90 GLU cc_start: 0.8539 (mm-30) cc_final: 0.7986 (tm-30) REVERT: C 123 ARG cc_start: 0.8797 (ttm170) cc_final: 0.8594 (tpp80) REVERT: C 145 THR cc_start: 0.7764 (m) cc_final: 0.7515 (m) REVERT: C 169 PHE cc_start: 0.8665 (m-80) cc_final: 0.8391 (m-80) REVERT: C 206 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8408 (m-40) REVERT: C 269 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8389 (pp) REVERT: C 399 TYR cc_start: 0.8985 (t80) cc_final: 0.8657 (t80) REVERT: C 417 GLU cc_start: 0.8615 (mp0) cc_final: 0.8315 (mp0) REVERT: E 90 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7881 (tp30) REVERT: E 248 LEU cc_start: 0.9131 (tp) cc_final: 0.8824 (tt) REVERT: E 249 ASN cc_start: 0.8599 (m-40) cc_final: 0.8302 (m-40) REVERT: E 408 TYR cc_start: 0.9286 (m-80) cc_final: 0.8894 (m-10) REVERT: E 430 LYS cc_start: 0.9545 (ttmt) cc_final: 0.9257 (tptt) REVERT: J 33 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8778 (p0) REVERT: J 36 MET cc_start: 0.8456 (ttp) cc_final: 0.8198 (tmm) REVERT: J 76 ASP cc_start: 0.8784 (m-30) cc_final: 0.8534 (m-30) REVERT: J 88 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.5283 (t70) REVERT: J 90 GLU cc_start: 0.8313 (tp30) cc_final: 0.8065 (tp30) REVERT: J 103 TYR cc_start: 0.8759 (t80) cc_final: 0.8492 (t80) REVERT: J 108 TYR cc_start: 0.9096 (m-80) cc_final: 0.8640 (m-80) REVERT: J 156 ARG cc_start: 0.9033 (mmt90) cc_final: 0.8801 (mmm-85) REVERT: J 327 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.9144 (p0) REVERT: J 346 TRP cc_start: 0.8593 (p-90) cc_final: 0.4580 (t-100) REVERT: J 413 MET cc_start: 0.8627 (tpp) cc_final: 0.8423 (mmm) REVERT: J 430 LYS cc_start: 0.9598 (ttmt) cc_final: 0.9228 (tptt) REVERT: J 432 TYR cc_start: 0.8650 (m-80) cc_final: 0.8030 (t80) REVERT: K 6 SER cc_start: 0.8994 (m) cc_final: 0.8749 (t) REVERT: K 71 GLU cc_start: 0.8141 (tt0) cc_final: 0.7842 (tt0) REVERT: K 90 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: K 154 MET cc_start: 0.8771 (mmm) cc_final: 0.8509 (mmm) REVERT: K 210 TYR cc_start: 0.8945 (m-10) cc_final: 0.8570 (m-80) REVERT: K 251 ASP cc_start: 0.8208 (p0) cc_final: 0.7953 (p0) REVERT: K 256 GLN cc_start: 0.9125 (pt0) cc_final: 0.8790 (tm-30) REVERT: K 287 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8160 (p) REVERT: K 300 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8747 (t0) REVERT: K 346 TRP cc_start: 0.8562 (p-90) cc_final: 0.4254 (t-100) REVERT: K 357 TYR cc_start: 0.8618 (m-80) cc_final: 0.8096 (m-80) REVERT: K 386 GLU cc_start: 0.8617 (tt0) cc_final: 0.8178 (pt0) REVERT: K 408 TYR cc_start: 0.8833 (m-80) cc_final: 0.8139 (m-80) REVERT: K 430 LYS cc_start: 0.9556 (ttmt) cc_final: 0.9132 (tptt) REVERT: K 432 TYR cc_start: 0.8610 (m-80) cc_final: 0.7877 (t80) REVERT: K 433 GLU cc_start: 0.9109 (tt0) cc_final: 0.8823 (tp30) REVERT: L 6 SER cc_start: 0.8930 (m) cc_final: 0.8711 (t) REVERT: L 69 ASP cc_start: 0.8728 (t0) cc_final: 0.8289 (t70) REVERT: L 76 ASP cc_start: 0.8880 (m-30) cc_final: 0.8632 (m-30) REVERT: L 90 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: L 108 TYR cc_start: 0.9208 (m-80) cc_final: 0.8798 (m-10) REVERT: L 145 THR cc_start: 0.7139 (m) cc_final: 0.6761 (m) REVERT: L 210 TYR cc_start: 0.8748 (m-10) cc_final: 0.8464 (m-80) REVERT: L 232 SER cc_start: 0.9256 (m) cc_final: 0.8883 (p) REVERT: L 346 TRP cc_start: 0.8347 (p-90) cc_final: 0.4522 (t-100) REVERT: L 372 GLN cc_start: 0.8861 (mp10) cc_final: 0.8615 (pm20) REVERT: L 394 LYS cc_start: 0.9311 (mppt) cc_final: 0.8956 (mppt) REVERT: L 432 TYR cc_start: 0.8580 (m-80) cc_final: 0.7900 (t80) REVERT: F 14 ASN cc_start: 0.8675 (m-40) cc_final: 0.8385 (m-40) REVERT: F 122 LYS cc_start: 0.9122 (pttp) cc_final: 0.8893 (ptmm) REVERT: F 129 CYS cc_start: 0.7358 (t) cc_final: 0.6831 (p) REVERT: F 156 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.6380 (tpp-160) REVERT: F 159 TYR cc_start: 0.8592 (m-80) cc_final: 0.8180 (m-80) REVERT: F 162 ARG cc_start: 0.8702 (mmt-90) cc_final: 0.8438 (mmp80) REVERT: F 164 MET cc_start: 0.8785 (mmm) cc_final: 0.8529 (mtm) REVERT: F 226 ASN cc_start: 0.9183 (m-40) cc_final: 0.8833 (m-40) REVERT: F 245 GLN cc_start: 0.8596 (mp10) cc_final: 0.8302 (mp10) REVERT: F 310 TYR cc_start: 0.9138 (m-80) cc_final: 0.8845 (m-80) REVERT: F 325 GLU cc_start: 0.8793 (tt0) cc_final: 0.8290 (pt0) REVERT: F 330 MET cc_start: 0.8713 (mmt) cc_final: 0.8438 (mmt) REVERT: F 333 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9166 (tp) REVERT: F 405 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 22 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7797 (tm-30) REVERT: D 26 ASP cc_start: 0.8396 (m-30) cc_final: 0.7901 (m-30) REVERT: D 86 ARG cc_start: 0.8762 (ttp80) cc_final: 0.8412 (ttp80) REVERT: D 103 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8515 (ttmt) REVERT: D 122 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9088 (ptpt) REVERT: D 156 ARG cc_start: 0.7904 (tpp-160) cc_final: 0.6994 (tpp-160) REVERT: D 164 MET cc_start: 0.8957 (mmm) cc_final: 0.8195 (mtt) REVERT: D 213 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.8016 (ttp-110) REVERT: D 282 ARG cc_start: 0.6005 (mmt180) cc_final: 0.5780 (mmp-170) REVERT: D 344 TRP cc_start: 0.8994 (OUTLIER) cc_final: 0.8017 (p-90) REVERT: D 363 MET cc_start: 0.8556 (pmm) cc_final: 0.8127 (pmm) REVERT: D 375 GLN cc_start: 0.8446 (pp30) cc_final: 0.7137 (pp30) REVERT: D 376 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8151 (mt-10) REVERT: D 379 LYS cc_start: 0.9442 (mtpt) cc_final: 0.8774 (mtpt) REVERT: D 392 LYS cc_start: 0.9164 (mmtp) cc_final: 0.8950 (mmtt) REVERT: D 404 ASP cc_start: 0.8767 (p0) cc_final: 0.8301 (p0) REVERT: D 410 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8503 (mt-10) REVERT: D 422 TYR cc_start: 0.9054 (OUTLIER) cc_final: 0.8170 (t80) REVERT: G 3 GLU cc_start: 0.6471 (mp0) cc_final: 0.5918 (mp0) REVERT: G 14 ASN cc_start: 0.8782 (m-40) cc_final: 0.8563 (m-40) REVERT: G 31 ASP cc_start: 0.8873 (m-30) cc_final: 0.8523 (m-30) REVERT: G 50 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: G 121 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8446 (mtm180) REVERT: G 156 ARG cc_start: 0.8274 (ttt180) cc_final: 0.8025 (ttt180) REVERT: G 209 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8539 (p0) REVERT: G 213 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7956 (ptp90) REVERT: G 216 LYS cc_start: 0.9160 (ttpt) cc_final: 0.8949 (tmmt) REVERT: G 226 ASN cc_start: 0.8937 (m-40) cc_final: 0.8669 (m-40) REVERT: G 276 ARG cc_start: 0.8170 (mmm160) cc_final: 0.7922 (mmm160) REVERT: G 291 GLN cc_start: 0.8716 (mp10) cc_final: 0.8423 (mp10) REVERT: G 310 TYR cc_start: 0.9161 (m-10) cc_final: 0.8911 (m-80) REVERT: G 370 ASN cc_start: 0.8600 (t0) cc_final: 0.8024 (t0) REVERT: G 388 MET cc_start: 0.5188 (mmt) cc_final: 0.4966 (mmt) REVERT: H 50 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: H 73 MET cc_start: 0.8646 (mmm) cc_final: 0.8287 (mtm) REVERT: H 77 ARG cc_start: 0.9235 (ttm170) cc_final: 0.8972 (ttm110) REVERT: H 111 GLU cc_start: 0.8902 (mp0) cc_final: 0.8628 (mp0) REVERT: H 174 LYS cc_start: 0.9338 (mptt) cc_final: 0.9089 (mppt) REVERT: H 195 ASN cc_start: 0.9124 (m-40) cc_final: 0.8917 (m-40) REVERT: H 208 TYR cc_start: 0.8950 (m-10) cc_final: 0.8616 (m-80) REVERT: H 274 THR cc_start: 0.8982 (p) cc_final: 0.8772 (t) REVERT: H 291 GLN cc_start: 0.8571 (mp10) cc_final: 0.8272 (mp10) REVERT: H 337 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7126 (t0) REVERT: H 344 TRP cc_start: 0.9081 (OUTLIER) cc_final: 0.8258 (p-90) REVERT: H 363 MET cc_start: 0.8396 (pmm) cc_final: 0.7850 (pmm) REVERT: H 370 ASN cc_start: 0.8439 (t0) cc_final: 0.8107 (t0) REVERT: H 379 LYS cc_start: 0.9451 (ttpt) cc_final: 0.9099 (mtmm) REVERT: H 390 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7841 (ttm110) REVERT: H 406 MET cc_start: 0.8119 (mmm) cc_final: 0.7616 (mmm) REVERT: H 426 GLN cc_start: 0.7708 (tt0) cc_final: 0.7415 (tm-30) REVERT: I 121 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8549 (mtm180) REVERT: I 279 GLN cc_start: 0.8624 (pt0) cc_final: 0.8098 (pt0) REVERT: I 321 MET cc_start: 0.8613 (ptp) cc_final: 0.8307 (ptp) REVERT: I 375 GLN cc_start: 0.8254 (pp30) cc_final: 0.6100 (pp30) REVERT: I 379 LYS cc_start: 0.9557 (ttmt) cc_final: 0.8874 (mtmm) REVERT: B 133 PHE cc_start: 0.7938 (m-80) cc_final: 0.7429 (m-80) REVERT: B 162 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.7961 (tpp-160) REVERT: B 329 GLN cc_start: 0.9005 (mm110) cc_final: 0.8688 (tp40) REVERT: B 363 MET cc_start: 0.8464 (pmm) cc_final: 0.8167 (pmm) REVERT: B 405 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8036 (tm-30) outliers start: 235 outliers final: 196 residues processed: 1575 average time/residue: 0.2316 time to fit residues: 600.1783 Evaluate side-chains 1641 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 1424 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 316 CYS Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 141 PHE Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 282 TYR Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 362 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 384 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 141 PHE Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 282 TYR Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 296 PHE Chi-restraints excluded: chain K residue 300 ASN Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 375 VAL Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain K residue 384 ILE Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 167 LEU Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 168 SER Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 335 SER Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain D residue 344 TRP Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 422 TYR Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 50 TYR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 122 LYS Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 197 ASP Chi-restraints excluded: chain G residue 202 ILE Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 247 ASN Chi-restraints excluded: chain G residue 266 PHE Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 374 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 266 PHE Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 344 TRP Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 118 ASP Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 203 ASP Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 240 LEU Chi-restraints excluded: chain I residue 286 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 325 GLU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 422 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 435 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 410 optimal weight: 1.9990 chunk 496 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 128 GLN ** C 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN C 285 GLN E 206 ASN E 256 GLN J 192 HIS ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 393 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** K 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 393 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS ** D 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 375 GLN ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN B 307 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.109032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092156 restraints weight = 89764.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.095482 restraints weight = 44843.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.097752 restraints weight = 27308.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.099364 restraints weight = 18728.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.100494 restraints weight = 13900.631| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 41998 Z= 0.142 Angle : 0.744 14.271 57035 Z= 0.372 Chirality : 0.046 0.252 6240 Planarity : 0.005 0.051 7411 Dihedral : 9.760 154.187 5843 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 4.03 % Allowed : 29.66 % Favored : 66.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.12), residues: 5136 helix: 1.07 (0.10), residues: 2490 sheet: -0.40 (0.20), residues: 744 loop : -1.51 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 339 TYR 0.055 0.001 TYR E 210 PHE 0.048 0.001 PHE L 255 TRP 0.021 0.002 TRP K 388 HIS 0.011 0.001 HIS B 6 Details of bonding type rmsd covalent geometry : bond 0.00317 (41998) covalent geometry : angle 0.74364 (57035) hydrogen bonds : bond 0.04217 ( 2184) hydrogen bonds : angle 4.89637 ( 6354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11248.69 seconds wall clock time: 193 minutes 27.96 seconds (11607.96 seconds total)