Starting phenix.real_space_refine on Sat Mar 7 09:55:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj7_25156/03_2026/7sj7_25156.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj7_25156/03_2026/7sj7_25156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sj7_25156/03_2026/7sj7_25156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj7_25156/03_2026/7sj7_25156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sj7_25156/03_2026/7sj7_25156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj7_25156/03_2026/7sj7_25156.map" } resolution = 3.8 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= 1.425 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 176 residue(s): 0.05s 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: 9.75, per 1000 atoms: 0.24 Number of scatterers: 41056 At special positions: 0 Unit cell: (170.2, 103.96, 211.6, 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: 3.63 Conformation dependent library (CDL) restraints added in 1.7 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: 222 helices and 36 sheets defined 53.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 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: 4.660A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) 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 128 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 removed outlier: 3.669A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.734A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 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: 3.878A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.611A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (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: 4.660A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) 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 128 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 removed outlier: 3.668A pdb=" N ILE C 209 " --> pdb=" O ASP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.734A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 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: 3.878A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 437 " --> pdb=" O GLU C 433 " (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: 4.660A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) 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 128 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 removed outlier: 3.668A pdb=" N ILE E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.735A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.651A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 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: 3.878A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 437 " --> pdb=" O GLU E 433 " (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: 4.660A pdb=" N ILE J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) 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 128 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 removed outlier: 3.669A pdb=" N ILE J 209 " --> pdb=" O ASP J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 244 removed outlier: 3.735A pdb=" N LEU J 227 " --> pdb=" O THR J 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 removed outlier: 3.651A pdb=" N VAL J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 297 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: 3.878A pdb=" N ALA J 387 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS J 401 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 removed outlier: 4.039A pdb=" N TYR J 408 " --> pdb=" O PHE J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL J 437 " --> pdb=" O GLU J 433 " (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: 4.659A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) 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 128 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 removed outlier: 3.669A pdb=" N ILE K 209 " --> pdb=" O ASP K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 244 removed outlier: 3.734A pdb=" N LEU K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 297 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: 3.878A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 411 removed outlier: 4.040A pdb=" N TYR K 408 " --> pdb=" O PHE K 404 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.611A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 437 " --> pdb=" O GLU K 433 " (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: 4.660A pdb=" N ILE L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) 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 128 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 removed outlier: 3.668A pdb=" N ILE L 209 " --> pdb=" O ASP L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.735A pdb=" N LEU L 227 " --> pdb=" O THR L 223 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 removed outlier: 3.652A pdb=" N VAL L 260 " --> pdb=" O GLN L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 297 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: 3.878A pdb=" N ALA L 387 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS L 401 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 removed outlier: 4.041A pdb=" N TYR L 408 " --> pdb=" O PHE L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 437 removed outlier: 3.612A pdb=" N PHE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.979A 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: 4.429A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.546A pdb=" N PHE F 90 " --> pdb=" O PRO F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 108 through 127 removed outlier: 3.860A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 5.085A 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: 3.519A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.350A 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 294 removed outlier: 3.700A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) 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 removed outlier: 3.634A pdb=" N ASN F 337 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 Processing helix chain 'F' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.866A 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: 4.179A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.979A 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: 4.429A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.086A 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: 3.518A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 5.349A 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 294 removed outlier: 3.700A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) 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 removed outlier: 3.634A pdb=" N ASN D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 400 removed outlier: 4.063A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.866A 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 41 through 46 removed outlier: 3.980A 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: 4.429A pdb=" N MET G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE G 90 " --> pdb=" O PRO G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 5.085A 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: 3.518A pdb=" N ASN G 184 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU G 225 " --> pdb=" O THR G 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) removed outlier: 5.349A 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 294 removed outlier: 3.700A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) 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 removed outlier: 3.634A pdb=" N ASN G 337 " --> pdb=" O ILE G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 341 Processing helix chain 'G' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG G 391 " --> pdb=" O ALA G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.866A 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: 4.179A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.980A 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: 4.429A pdb=" N MET H 73 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE H 90 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 127 removed outlier: 3.860A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 5.085A 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: 3.518A pdb=" N ASN H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU H 225 " --> pdb=" O THR H 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) removed outlier: 5.350A 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 294 removed outlier: 3.700A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) 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 removed outlier: 3.634A pdb=" N ASN H 337 " --> pdb=" O ILE H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 341 Processing helix chain 'H' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.866A 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 41 through 46 removed outlier: 3.979A 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: 4.430A pdb=" N MET I 73 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.546A pdb=" N PHE I 90 " --> pdb=" O PRO I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 5.085A 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: 3.518A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 5.349A 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 294 removed outlier: 3.700A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) 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 removed outlier: 3.633A pdb=" N ASN I 337 " --> pdb=" O ILE I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 341 Processing helix chain 'I' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG I 391 " --> pdb=" O ALA I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.865A 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 41 through 46 removed outlier: 3.979A 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: 4.430A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.547A pdb=" N PHE B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 127 removed outlier: 3.859A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.085A 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: 3.518A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.575A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.350A 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 294 removed outlier: 3.700A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) 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 removed outlier: 3.634A pdb=" N ASN B 337 " --> pdb=" O ILE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.633A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.062A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.866A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 removed outlier: 8.901A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) 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 93 through 94 removed outlier: 8.901A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) 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 93 through 94 removed outlier: 8.902A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) 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 93 through 94 removed outlier: 8.901A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) 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 93 through 94 removed outlier: 8.901A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) 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 93 through 94 removed outlier: 8.902A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) 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: 8.191A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 65 " --> pdb=" O ILE F 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 4.635A 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: 8.191A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 65 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.636A 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: 8.191A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 163 " --> pdb=" O GLN G 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU G 65 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 163 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET G 164 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR G 200 " --> pdb=" O MET G 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR G 166 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 4.636A 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: 8.192A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 91 through 92 removed outlier: 8.192A pdb=" N ILE H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU H 65 " --> pdb=" O ILE H 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 4.636A 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: 8.191A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU I 65 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET I 164 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR I 200 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR I 166 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.635A 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: 8.191A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 91 through 92 removed outlier: 8.191A pdb=" N ILE B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU B 65 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.635A 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 2160 hydrogen bonds defined for protein. 6192 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: 9.78 Time building geometry restraints manager: 4.63 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: 13615 1.34 - 1.46: 7555 1.46 - 1.57: 20336 1.57 - 1.69: 48 1.69 - 1.81: 444 Bond restraints: 41998 Sorted by residual: bond pdb=" N ARG I 359 " pdb=" CA ARG I 359 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.96e+00 bond pdb=" N ARG B 359 " pdb=" CA ARG B 359 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.30e+00 bond pdb=" N ARG G 359 " pdb=" CA ARG G 359 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.92e+00 bond pdb=" N ARG D 359 " pdb=" CA ARG D 359 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.21e+00 bond pdb=" C5 GDP I 501 " pdb=" C4 GDP I 501 " ideal model delta sigma weight residual 1.490 1.459 0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 41993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 56388 2.41 - 4.83: 578 4.83 - 7.24: 62 7.24 - 9.65: 6 9.65 - 12.06: 1 Bond angle restraints: 57035 Sorted by residual: angle pdb=" N ARG F 359 " pdb=" CA ARG F 359 " pdb=" C ARG F 359 " ideal model delta sigma weight residual 110.30 122.36 -12.06 1.50e+00 4.44e-01 6.47e+01 angle pdb=" C PRO H 357 " pdb=" N PRO H 358 " pdb=" CA PRO H 358 " ideal model delta sigma weight residual 119.84 126.58 -6.74 1.25e+00 6.40e-01 2.91e+01 angle pdb=" N PRO F 358 " pdb=" CA PRO F 358 " pdb=" C PRO F 358 " ideal model delta sigma weight residual 111.19 103.26 7.93 1.57e+00 4.06e-01 2.55e+01 angle pdb=" N VAL J 181 " pdb=" CA VAL J 181 " pdb=" C VAL J 181 " ideal model delta sigma weight residual 113.53 109.10 4.43 9.80e-01 1.04e+00 2.04e+01 angle pdb=" N VAL L 181 " pdb=" CA VAL L 181 " pdb=" C VAL L 181 " ideal model delta sigma weight residual 113.53 109.10 4.43 9.80e-01 1.04e+00 2.04e+01 ... (remaining 57030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.71: 24430 32.71 - 65.41: 455 65.41 - 98.12: 48 98.12 - 130.83: 6 130.83 - 163.53: 6 Dihedral angle restraints: 24945 sinusoidal: 9957 harmonic: 14988 Sorted by residual: dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -127.20 -163.53 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -127.24 -163.50 1 2.00e+01 2.50e-03 4.70e+01 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 -127.24 -163.49 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 24942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5514 0.071 - 0.142: 713 0.142 - 0.214: 6 0.214 - 0.285: 2 0.285 - 0.356: 5 Chirality restraints: 6240 Sorted by residual: 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 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 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 2.60e+00 chirality pdb=" CA ARG D 359 " pdb=" N ARG D 359 " pdb=" C ARG D 359 " pdb=" CB ARG D 359 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 6237 not shown) Planarity restraints: 7411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 357 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C PRO H 357 " -0.038 2.00e-02 2.50e+03 pdb=" O PRO H 357 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO H 358 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO I 357 " -0.011 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C PRO I 357 " 0.036 2.00e-02 2.50e+03 pdb=" O PRO I 357 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO I 358 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 357 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C PRO F 357 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO F 357 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO F 358 " 0.012 2.00e-02 2.50e+03 ... (remaining 7408 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 566 2.54 - 3.13: 34585 3.13 - 3.72: 65253 3.72 - 4.31: 88992 4.31 - 4.90: 151927 Nonbonded interactions: 341323 Sorted by model distance: nonbonded pdb=" O3B GTP K 501 " pdb="MG MG K 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP J 501 " pdb="MG MG J 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP E 501 " pdb="MG MG E 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP A 501 " pdb="MG MG A 502 " model vdw 1.947 2.170 nonbonded pdb=" O3B GTP L 501 " pdb="MG MG L 502 " model vdw 1.948 2.170 ... (remaining 341318 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: 11.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 38.120 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 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 : 0.006 0.064 41998 Z= 0.273 Angle : 0.665 12.064 57035 Z= 0.377 Chirality : 0.045 0.356 6240 Planarity : 0.004 0.032 7411 Dihedral : 13.533 163.533 15321 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.89 % Favored : 95.02 % Rotamer: Outliers : 5.43 % Allowed : 7.88 % Favored : 86.69 % 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: 0.52 (0.10), residues: 2430 sheet: -1.76 (0.19), residues: 732 loop : -1.68 (0.15), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 380 TYR 0.011 0.001 TYR L 272 PHE 0.015 0.002 PHE B 20 TRP 0.010 0.002 TRP G 21 HIS 0.004 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00581 (41998) covalent geometry : angle 0.66454 (57035) hydrogen bonds : bond 0.14192 ( 2124) hydrogen bonds : angle 6.71522 ( 6192) *********************** 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 1953 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 1713 time to evaluate : 1.613 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: A 25 CYS cc_start: 0.7918 (m) cc_final: 0.7707 (m) REVERT: A 33 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7209 (p0) REVERT: A 90 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: A 198 SER cc_start: 0.8638 (p) cc_final: 0.8044 (p) REVERT: A 221 ARG cc_start: 0.7099 (mtt90) cc_final: 0.6718 (mtt90) REVERT: A 280 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7926 (ttpt) REVERT: A 300 ASN cc_start: 0.8390 (m-40) cc_final: 0.8176 (t0) REVERT: A 318 LEU cc_start: 0.8957 (mt) cc_final: 0.8664 (mp) REVERT: A 336 LYS cc_start: 0.9038 (mtpm) cc_final: 0.8831 (mtpp) REVERT: A 382 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8413 (p) REVERT: A 392 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7638 (t0) REVERT: C 33 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6924 (p0) REVERT: C 50 ASN cc_start: 0.7804 (t0) cc_final: 0.7198 (t0) REVERT: C 103 TYR cc_start: 0.8833 (t80) cc_final: 0.8253 (t80) REVERT: C 121 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7810 (tpt170) REVERT: C 154 MET cc_start: 0.8886 (mmm) cc_final: 0.8666 (mmm) REVERT: C 210 TYR cc_start: 0.8391 (m-10) cc_final: 0.8072 (m-80) REVERT: C 228 ASN cc_start: 0.8569 (m-40) cc_final: 0.8342 (m-40) REVERT: C 256 GLN cc_start: 0.8277 (pt0) cc_final: 0.7998 (pt0) REVERT: C 304 LYS cc_start: 0.9084 (tppt) cc_final: 0.8825 (tptt) REVERT: C 305 CYS cc_start: 0.7788 (m) cc_final: 0.7529 (m) REVERT: C 317 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8870 (mt) REVERT: C 322 ASP cc_start: 0.7820 (t0) cc_final: 0.7397 (t70) REVERT: C 382 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 392 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7642 (t0) REVERT: C 429 GLU cc_start: 0.8368 (tp30) cc_final: 0.8128 (tm-30) REVERT: E 30 ILE cc_start: 0.8493 (mm) cc_final: 0.8279 (mm) REVERT: E 33 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6405 (p0) REVERT: E 71 GLU cc_start: 0.7263 (pt0) cc_final: 0.7019 (pt0) REVERT: E 103 TYR cc_start: 0.8698 (t80) cc_final: 0.8402 (t80) REVERT: E 121 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7847 (tpt170) REVERT: E 219 ILE cc_start: 0.8472 (mt) cc_final: 0.7362 (pt) REVERT: E 256 GLN cc_start: 0.8327 (pt0) cc_final: 0.8085 (pt0) REVERT: E 269 LEU cc_start: 0.8867 (pp) cc_final: 0.8631 (pp) REVERT: E 305 CYS cc_start: 0.7958 (m) cc_final: 0.7283 (m) REVERT: E 322 ASP cc_start: 0.7834 (t0) cc_final: 0.7604 (t70) REVERT: E 336 LYS cc_start: 0.8971 (mtpm) cc_final: 0.8618 (mtpp) REVERT: E 352 LYS cc_start: 0.8635 (tttp) cc_final: 0.8201 (tppt) REVERT: E 382 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8196 (p) REVERT: E 386 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: E 392 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7942 (t0) REVERT: E 413 MET cc_start: 0.6545 (ttm) cc_final: 0.6083 (mtp) REVERT: J 3 GLU cc_start: 0.7216 (mp0) cc_final: 0.6794 (mm-30) REVERT: J 50 ASN cc_start: 0.7911 (t0) cc_final: 0.7188 (t0) REVERT: J 51 THR cc_start: 0.8536 (p) cc_final: 0.8286 (p) REVERT: J 75 ILE cc_start: 0.9124 (mm) cc_final: 0.8855 (mt) REVERT: J 103 TYR cc_start: 0.8840 (t80) cc_final: 0.8375 (t80) REVERT: J 109 THR cc_start: 0.9487 (m) cc_final: 0.8369 (p) REVERT: J 149 PHE cc_start: 0.9263 (t80) cc_final: 0.9012 (t80) REVERT: J 198 SER cc_start: 0.8461 (p) cc_final: 0.8042 (t) REVERT: J 207 GLU cc_start: 0.8365 (tt0) cc_final: 0.8162 (tt0) REVERT: J 290 GLU cc_start: 0.8344 (tt0) cc_final: 0.8060 (tm-30) REVERT: J 305 CYS cc_start: 0.7815 (m) cc_final: 0.7451 (m) REVERT: J 317 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8861 (mt) REVERT: J 326 LYS cc_start: 0.9030 (tttm) cc_final: 0.8649 (ptpt) REVERT: J 352 LYS cc_start: 0.8328 (tttp) cc_final: 0.8027 (tppt) REVERT: J 357 TYR cc_start: 0.8675 (m-80) cc_final: 0.8375 (m-80) REVERT: J 382 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8257 (p) REVERT: J 392 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8126 (t0) REVERT: J 417 GLU cc_start: 0.7891 (tt0) cc_final: 0.7594 (tt0) REVERT: J 434 GLU cc_start: 0.8950 (tt0) cc_final: 0.8744 (tt0) REVERT: K 50 ASN cc_start: 0.7881 (t0) cc_final: 0.7266 (t0) REVERT: K 90 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: K 110 ILE cc_start: 0.9314 (mm) cc_final: 0.8781 (mm) REVERT: K 151 SER cc_start: 0.9023 (m) cc_final: 0.8786 (p) REVERT: K 198 SER cc_start: 0.8378 (p) cc_final: 0.7851 (p) REVERT: K 207 GLU cc_start: 0.8084 (tt0) cc_final: 0.7840 (tt0) REVERT: K 280 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8377 (ttpt) REVERT: K 326 LYS cc_start: 0.8899 (tttm) cc_final: 0.8654 (ptpt) REVERT: K 352 LYS cc_start: 0.8152 (tttp) cc_final: 0.7823 (tppt) REVERT: K 382 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8229 (p) REVERT: K 392 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7981 (t0) REVERT: K 429 GLU cc_start: 0.8544 (tp30) cc_final: 0.8273 (tp30) REVERT: L 90 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7613 (tm-30) REVERT: L 110 ILE cc_start: 0.9366 (mm) cc_final: 0.8905 (mm) REVERT: L 198 SER cc_start: 0.8409 (p) cc_final: 0.7493 (p) REVERT: L 205 ASP cc_start: 0.8447 (t0) cc_final: 0.8197 (t0) REVERT: L 206 ASN cc_start: 0.8754 (m110) cc_final: 0.8407 (m-40) REVERT: L 210 TYR cc_start: 0.8424 (m-10) cc_final: 0.7984 (m-80) REVERT: L 305 CYS cc_start: 0.8063 (m) cc_final: 0.7629 (m) REVERT: L 326 LYS cc_start: 0.8990 (tttm) cc_final: 0.8391 (mttt) REVERT: L 336 LYS cc_start: 0.8881 (mtpm) cc_final: 0.8530 (mtpp) REVERT: L 352 LYS cc_start: 0.8260 (tttp) cc_final: 0.7896 (tppt) REVERT: L 372 GLN cc_start: 0.7934 (mt0) cc_final: 0.7166 (pt0) REVERT: L 386 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8406 (pp20) REVERT: L 392 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8375 (t0) REVERT: F 22 GLU cc_start: 0.7711 (tt0) cc_final: 0.7445 (tm-30) REVERT: F 26 ASP cc_start: 0.8354 (m-30) cc_final: 0.6663 (m-30) REVERT: F 36 TYR cc_start: 0.8324 (t80) cc_final: 0.7628 (t80) REVERT: F 58 LYS cc_start: 0.7384 (mttt) cc_final: 0.7078 (mtpt) REVERT: F 106 TYR cc_start: 0.8743 (m-80) cc_final: 0.8429 (m-10) REVERT: F 108 GLU cc_start: 0.8471 (tp30) cc_final: 0.8221 (tm-30) REVERT: F 112 LEU cc_start: 0.8475 (mp) cc_final: 0.8165 (tp) REVERT: F 174 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8213 (mtpt) REVERT: F 198 GLU cc_start: 0.8419 (pt0) cc_final: 0.8102 (pt0) REVERT: F 200 TYR cc_start: 0.9018 (m-80) cc_final: 0.8704 (m-10) REVERT: F 208 TYR cc_start: 0.8496 (m-10) cc_final: 0.7841 (m-80) REVERT: F 252 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8170 (mtpt) REVERT: F 288 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7197 (tm-30) REVERT: F 304 ASP cc_start: 0.8261 (t0) cc_final: 0.8024 (t0) REVERT: F 327 ASP cc_start: 0.8403 (m-30) cc_final: 0.8081 (m-30) REVERT: F 329 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8830 (mm-40) REVERT: D 26 ASP cc_start: 0.8488 (m-30) cc_final: 0.7106 (m-30) REVERT: D 108 GLU cc_start: 0.8435 (tp30) cc_final: 0.8211 (tp30) REVERT: D 111 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7081 (mt-10) REVERT: D 122 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8781 (ttmt) REVERT: D 198 GLU cc_start: 0.8279 (pt0) cc_final: 0.7965 (pt0) REVERT: D 208 TYR cc_start: 0.8506 (m-10) cc_final: 0.8123 (m-80) REVERT: D 379 LYS cc_start: 0.8825 (mtpt) cc_final: 0.7881 (ttmt) REVERT: G 31 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8448 (t0) REVERT: G 36 TYR cc_start: 0.8213 (t80) cc_final: 0.7699 (t80) REVERT: G 103 LYS cc_start: 0.8107 (mttt) cc_final: 0.7851 (mtpp) REVERT: G 159 TYR cc_start: 0.8731 (m-80) cc_final: 0.8432 (m-80) REVERT: G 198 GLU cc_start: 0.8403 (pt0) cc_final: 0.8043 (pt0) REVERT: G 298 ASN cc_start: 0.9187 (t0) cc_final: 0.8734 (t0) REVERT: G 299 MET cc_start: 0.8516 (mmp) cc_final: 0.8127 (mmp) REVERT: G 310 TYR cc_start: 0.9149 (m-80) cc_final: 0.8922 (m-80) REVERT: G 388 MET cc_start: 0.8314 (mtp) cc_final: 0.7921 (mmt) REVERT: G 397 TRP cc_start: 0.8688 (m100) cc_final: 0.8461 (m-10) REVERT: H 108 GLU cc_start: 0.8490 (tp30) cc_final: 0.8229 (tp30) REVERT: H 118 ASP cc_start: 0.8264 (m-30) cc_final: 0.8027 (m-30) REVERT: H 125 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7910 (mp0) REVERT: H 129 CYS cc_start: 0.7926 (t) cc_final: 0.7474 (t) REVERT: H 162 ARG cc_start: 0.9057 (mmt-90) cc_final: 0.8749 (mmp80) REVERT: H 177 ASP cc_start: 0.7769 (t70) cc_final: 0.7544 (t0) REVERT: H 200 TYR cc_start: 0.8923 (m-80) cc_final: 0.8719 (m-10) REVERT: H 291 GLN cc_start: 0.8795 (pt0) cc_final: 0.8588 (pm20) REVERT: H 325 GLU cc_start: 0.7807 (tt0) cc_final: 0.6782 (tt0) REVERT: H 397 TRP cc_start: 0.8570 (m100) cc_final: 0.7801 (m-10) REVERT: I 26 ASP cc_start: 0.8229 (m-30) cc_final: 0.7247 (m-30) REVERT: I 30 ILE cc_start: 0.8680 (mm) cc_final: 0.8366 (mm) REVERT: I 95 SER cc_start: 0.9326 (m) cc_final: 0.8976 (p) REVERT: I 103 LYS cc_start: 0.8176 (mttt) cc_final: 0.7942 (mtpp) REVERT: I 106 TYR cc_start: 0.8638 (m-80) cc_final: 0.8216 (m-10) REVERT: I 118 ASP cc_start: 0.8444 (m-30) cc_final: 0.8190 (m-30) REVERT: I 125 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8079 (mp0) REVERT: I 159 TYR cc_start: 0.8650 (m-80) cc_final: 0.8069 (m-80) REVERT: I 200 TYR cc_start: 0.9025 (m-80) cc_final: 0.8763 (m-10) REVERT: I 209 ASP cc_start: 0.8502 (t0) cc_final: 0.8291 (t0) REVERT: I 257 MET cc_start: 0.8452 (mmp) cc_final: 0.8112 (mmm) REVERT: I 304 ASP cc_start: 0.8646 (t0) cc_final: 0.8265 (t0) REVERT: I 419 VAL cc_start: 0.9325 (t) cc_final: 0.9020 (p) REVERT: I 422 TYR cc_start: 0.8167 (m-80) cc_final: 0.7937 (m-80) REVERT: B 31 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8564 (m-30) REVERT: B 37 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7981 (p) REVERT: B 106 TYR cc_start: 0.8648 (m-80) cc_final: 0.8428 (m-80) REVERT: B 108 GLU cc_start: 0.8181 (tp30) cc_final: 0.7802 (tp30) REVERT: B 112 LEU cc_start: 0.8097 (mp) cc_final: 0.7827 (tp) REVERT: B 121 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8461 (mtm-85) REVERT: B 138 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8724 (m) REVERT: B 198 GLU cc_start: 0.8144 (pt0) cc_final: 0.7564 (pt0) REVERT: B 200 TYR cc_start: 0.8970 (m-80) cc_final: 0.8323 (m-10) REVERT: B 213 ARG cc_start: 0.8154 (ttm110) cc_final: 0.7829 (ttp-170) outliers start: 240 outliers final: 92 residues processed: 1876 average time/residue: 0.2582 time to fit residues: 778.8590 Evaluate side-chains 1359 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1241 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 200 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 73 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 200 CYS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 363 VAL 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 E residue 392 ASP Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 339 ARG Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 382 THR Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 73 THR 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 200 CYS Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 287 SER Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 339 ARG Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 382 THR Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 141 PHE Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 156 ARG Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 303 CYS Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 494 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN C 300 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN E 300 ASN J 176 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN K 186 ASN L 88 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 347 ASN H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS I 245 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 245 GLN B 279 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.120681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.099920 restraints weight = 66190.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.103499 restraints weight = 35802.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.105980 restraints weight = 23188.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107722 restraints weight = 16844.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108985 restraints weight = 13218.452| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2275 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= 0.194 Angle : 0.650 6.928 57035 Z= 0.333 Chirality : 0.046 0.174 6240 Planarity : 0.005 0.067 7411 Dihedral : 11.473 165.441 5952 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.54 % Favored : 96.40 % Rotamer: Outliers : 5.07 % Allowed : 16.59 % Favored : 78.33 % 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: -0.29 (0.12), residues: 5136 helix: 1.18 (0.10), residues: 2412 sheet: -1.31 (0.19), residues: 720 loop : -1.43 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 213 TYR 0.029 0.002 TYR F 425 PHE 0.034 0.002 PHE I 81 TRP 0.012 0.002 TRP B 21 HIS 0.010 0.001 HIS I 6 Details of bonding type rmsd covalent geometry : bond 0.00437 (41998) covalent geometry : angle 0.64998 (57035) hydrogen bonds : bond 0.04910 ( 2124) hydrogen bonds : angle 5.14122 ( 6192) *********************** 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 1599 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 1375 time to evaluate : 1.568 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: A 90 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: A 113 GLU cc_start: 0.7496 (mp0) cc_final: 0.7037 (mp0) REVERT: A 256 GLN cc_start: 0.8278 (pt0) cc_final: 0.7844 (pt0) REVERT: A 257 THR cc_start: 0.8821 (m) cc_final: 0.8488 (m) REVERT: A 392 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7700 (t0) REVERT: A 411 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7697 (tp30) REVERT: C 50 ASN cc_start: 0.7924 (t0) cc_final: 0.7650 (t0) REVERT: C 90 GLU cc_start: 0.8064 (tp30) cc_final: 0.7837 (tp30) REVERT: C 103 TYR cc_start: 0.8775 (t80) cc_final: 0.8281 (t80) REVERT: C 121 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7806 (tpt170) REVERT: C 154 MET cc_start: 0.8737 (mmm) cc_final: 0.8444 (mmm) REVERT: C 210 TYR cc_start: 0.8364 (m-10) cc_final: 0.7960 (m-80) REVERT: C 228 ASN cc_start: 0.8527 (m-40) cc_final: 0.8292 (m-40) REVERT: C 256 GLN cc_start: 0.8236 (pt0) cc_final: 0.7814 (pt0) REVERT: C 286 LEU cc_start: 0.8355 (mm) cc_final: 0.8103 (pp) REVERT: C 300 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8227 (t0) REVERT: C 304 LYS cc_start: 0.9071 (tppt) cc_final: 0.8801 (tptt) REVERT: C 317 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8786 (mt) REVERT: C 322 ASP cc_start: 0.7741 (t0) cc_final: 0.7361 (t70) REVERT: C 392 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7585 (t0) REVERT: E 156 ARG cc_start: 0.8783 (mmt-90) cc_final: 0.8320 (mmm-85) REVERT: E 228 ASN cc_start: 0.8584 (m-40) cc_final: 0.8372 (m-40) REVERT: E 256 GLN cc_start: 0.8206 (pt0) cc_final: 0.7703 (pt0) REVERT: E 269 LEU cc_start: 0.8816 (pp) cc_final: 0.8513 (pp) REVERT: E 305 CYS cc_start: 0.7772 (m) cc_final: 0.7294 (m) REVERT: E 322 ASP cc_start: 0.7736 (t0) cc_final: 0.7512 (t70) REVERT: E 336 LYS cc_start: 0.8949 (mtpm) cc_final: 0.8605 (mtpp) REVERT: E 392 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7716 (t0) REVERT: J 75 ILE cc_start: 0.9110 (mm) cc_final: 0.8799 (mt) REVERT: J 90 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7892 (tp30) REVERT: J 103 TYR cc_start: 0.8823 (t80) cc_final: 0.8444 (t80) REVERT: J 243 ARG cc_start: 0.8907 (mtm110) cc_final: 0.8706 (mtm110) REVERT: J 286 LEU cc_start: 0.8559 (mt) cc_final: 0.8203 (pp) REVERT: J 293 ASN cc_start: 0.8715 (m-40) cc_final: 0.8242 (m110) REVERT: J 317 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8792 (mt) REVERT: J 326 LYS cc_start: 0.8957 (tttm) cc_final: 0.8385 (pttt) REVERT: J 352 LYS cc_start: 0.8243 (tttp) cc_final: 0.7794 (tppt) REVERT: J 357 TYR cc_start: 0.8487 (m-80) cc_final: 0.8075 (m-80) REVERT: J 377 MET cc_start: 0.8928 (ttp) cc_final: 0.8480 (tmm) REVERT: J 392 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8123 (t0) REVERT: K 3 GLU cc_start: 0.6371 (mm-30) cc_final: 0.6097 (mm-30) REVERT: K 50 ASN cc_start: 0.8204 (t0) cc_final: 0.7930 (t0) REVERT: K 90 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: K 110 ILE cc_start: 0.9224 (mm) cc_final: 0.9016 (mm) REVERT: K 113 GLU cc_start: 0.8273 (mp0) cc_final: 0.7994 (mp0) REVERT: K 199 ASP cc_start: 0.8242 (m-30) cc_final: 0.8005 (t0) REVERT: K 326 LYS cc_start: 0.8854 (tttm) cc_final: 0.8466 (ptpt) REVERT: K 352 LYS cc_start: 0.8117 (tttp) cc_final: 0.7727 (tppt) REVERT: K 357 TYR cc_start: 0.8256 (m-80) cc_final: 0.7874 (m-80) REVERT: K 377 MET cc_start: 0.8836 (ttp) cc_final: 0.8551 (tmm) REVERT: K 392 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7928 (t0) REVERT: L 50 ASN cc_start: 0.8595 (t0) cc_final: 0.8365 (t0) REVERT: L 76 ASP cc_start: 0.8683 (m-30) cc_final: 0.8251 (m-30) REVERT: L 90 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7663 (tp30) REVERT: L 103 TYR cc_start: 0.8722 (t80) cc_final: 0.8461 (t80) REVERT: L 205 ASP cc_start: 0.8271 (t0) cc_final: 0.7649 (t70) REVERT: L 206 ASN cc_start: 0.8494 (m110) cc_final: 0.7709 (m-40) REVERT: L 210 TYR cc_start: 0.8346 (m-10) cc_final: 0.7919 (m-80) REVERT: L 243 ARG cc_start: 0.9010 (mtm110) cc_final: 0.8745 (mtm110) REVERT: L 300 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8391 (t0) REVERT: L 305 CYS cc_start: 0.7816 (m) cc_final: 0.7289 (m) REVERT: L 326 LYS cc_start: 0.8850 (tttm) cc_final: 0.8296 (pttt) REVERT: L 357 TYR cc_start: 0.8461 (m-80) cc_final: 0.8057 (m-80) REVERT: L 372 GLN cc_start: 0.7938 (mt0) cc_final: 0.7189 (pt0) REVERT: L 386 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8245 (pp20) REVERT: L 392 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8138 (t0) REVERT: L 425 MET cc_start: 0.8825 (mmp) cc_final: 0.8585 (mmp) REVERT: F 14 ASN cc_start: 0.8634 (m-40) cc_final: 0.8280 (m-40) REVERT: F 19 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8727 (mmmt) REVERT: F 36 TYR cc_start: 0.8271 (t80) cc_final: 0.7816 (t80) REVERT: F 46 ARG cc_start: 0.8692 (mmt-90) cc_final: 0.8448 (mmt-90) REVERT: F 106 TYR cc_start: 0.8607 (m-80) cc_final: 0.8333 (m-10) REVERT: F 112 LEU cc_start: 0.8449 (mp) cc_final: 0.8188 (tp) REVERT: F 136 THR cc_start: 0.8975 (m) cc_final: 0.8644 (p) REVERT: F 208 TYR cc_start: 0.8339 (m-10) cc_final: 0.7857 (m-80) REVERT: F 249 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.7992 (p0) REVERT: F 323 MET cc_start: 0.7557 (mmm) cc_final: 0.7328 (mmm) REVERT: D 26 ASP cc_start: 0.8033 (m-30) cc_final: 0.7706 (m-30) REVERT: D 58 LYS cc_start: 0.7289 (mtpt) cc_final: 0.6860 (mtpt) REVERT: D 111 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7085 (mt-10) REVERT: D 112 LEU cc_start: 0.8224 (tp) cc_final: 0.7999 (tp) REVERT: D 122 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8761 (ttmt) REVERT: D 136 THR cc_start: 0.8957 (m) cc_final: 0.8682 (p) REVERT: D 198 GLU cc_start: 0.8295 (pt0) cc_final: 0.7962 (pt0) REVERT: D 208 TYR cc_start: 0.8315 (m-10) cc_final: 0.8056 (m-80) REVERT: D 209 ASP cc_start: 0.8723 (t0) cc_final: 0.8192 (t0) REVERT: D 249 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8356 (p0) REVERT: D 291 GLN cc_start: 0.8164 (mp10) cc_final: 0.7945 (mp10) REVERT: D 298 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8711 (t0) REVERT: D 307 HIS cc_start: 0.8727 (m-70) cc_final: 0.8463 (m90) REVERT: D 425 TYR cc_start: 0.8749 (m-80) cc_final: 0.7939 (m-80) REVERT: G 31 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8530 (t0) REVERT: G 36 TYR cc_start: 0.8233 (t80) cc_final: 0.7863 (t80) REVERT: G 103 LYS cc_start: 0.8298 (mttt) cc_final: 0.8017 (mtpp) REVERT: G 116 VAL cc_start: 0.9100 (t) cc_final: 0.8888 (p) REVERT: G 158 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7958 (tt0) REVERT: G 159 TYR cc_start: 0.8655 (m-80) cc_final: 0.7810 (m-80) REVERT: G 245 GLN cc_start: 0.8478 (mt0) cc_final: 0.7987 (mt0) REVERT: G 249 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8365 (p0) REVERT: G 257 MET cc_start: 0.8683 (mmp) cc_final: 0.8227 (mmm) REVERT: G 299 MET cc_start: 0.8751 (mmp) cc_final: 0.8370 (mmp) REVERT: G 304 ASP cc_start: 0.8420 (t0) cc_final: 0.8098 (t70) REVERT: G 306 ARG cc_start: 0.9186 (mpp80) cc_final: 0.8885 (mtm-85) REVERT: G 310 TYR cc_start: 0.9182 (m-80) cc_final: 0.8868 (m-80) REVERT: G 375 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7862 (pp30) REVERT: G 379 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9090 (ttpt) REVERT: G 388 MET cc_start: 0.8356 (mtp) cc_final: 0.7931 (mmt) REVERT: H 36 TYR cc_start: 0.8214 (t80) cc_final: 0.7871 (t80) REVERT: H 129 CYS cc_start: 0.8042 (t) cc_final: 0.7682 (t) REVERT: H 177 ASP cc_start: 0.7624 (t70) cc_final: 0.7410 (t0) REVERT: H 209 ASP cc_start: 0.8558 (t0) cc_final: 0.7833 (t0) REVERT: H 249 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8307 (p0) REVERT: H 291 GLN cc_start: 0.8737 (pt0) cc_final: 0.8531 (pm20) REVERT: H 322 SER cc_start: 0.8171 (m) cc_final: 0.7879 (p) REVERT: H 397 TRP cc_start: 0.8679 (m100) cc_final: 0.7757 (m-10) REVERT: H 407 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8453 (mp0) REVERT: I 26 ASP cc_start: 0.7764 (m-30) cc_final: 0.7534 (m-30) REVERT: I 31 ASP cc_start: 0.8776 (t0) cc_final: 0.8151 (t0) REVERT: I 95 SER cc_start: 0.9301 (m) cc_final: 0.9018 (p) REVERT: I 158 GLU cc_start: 0.8110 (tt0) cc_final: 0.7824 (tt0) REVERT: I 198 GLU cc_start: 0.8122 (pt0) cc_final: 0.7305 (pt0) REVERT: I 200 TYR cc_start: 0.8956 (m-80) cc_final: 0.8434 (m-10) REVERT: I 257 MET cc_start: 0.8624 (mmp) cc_final: 0.8079 (mmm) REVERT: I 267 MET cc_start: 0.8710 (mtp) cc_final: 0.8347 (mtt) REVERT: I 419 VAL cc_start: 0.9310 (t) cc_final: 0.9070 (p) REVERT: B 31 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8575 (m-30) REVERT: B 37 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7977 (p) REVERT: B 99 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8534 (m-40) REVERT: B 121 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8465 (mtm-85) REVERT: B 136 THR cc_start: 0.9012 (m) cc_final: 0.8594 (p) REVERT: B 209 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8079 (t0) REVERT: B 249 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8071 (p0) outliers start: 224 outliers final: 122 residues processed: 1517 average time/residue: 0.2542 time to fit residues: 626.6209 Evaluate side-chains 1341 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1190 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 356 ASN Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 22 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 141 PHE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 327 ASP Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 217 LEU 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 317 LEU Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 356 ASN Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain L residue 90 GLU 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 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 300 ASN Chi-restraints excluded: chain L residue 356 ASN Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 386 GLU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 421 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 190 HIS Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 362 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 452 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 361 optimal weight: 7.9990 chunk 279 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 392 optimal weight: 6.9990 chunk 244 optimal weight: 0.3980 chunk 480 optimal weight: 8.9990 chunk 384 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 300 ASN C 300 ASN J 101 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN L 88 HIS L 101 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 HIS F 99 ASN F 245 GLN F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN F 424 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** D 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN G 423 GLN G 424 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 298 ASN H 347 ASN H 375 GLN H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS I 375 GLN I 424 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B 307 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097619 restraints weight = 67097.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.101120 restraints weight = 36607.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.103573 restraints weight = 23910.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105319 restraints weight = 17470.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106597 restraints weight = 13736.103| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 41998 Z= 0.213 Angle : 0.647 7.660 57035 Z= 0.330 Chirality : 0.046 0.167 6240 Planarity : 0.004 0.061 7411 Dihedral : 11.213 164.785 5881 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 5.50 % Allowed : 18.90 % Favored : 75.59 % 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: -0.14 (0.12), residues: 5136 helix: 1.26 (0.11), residues: 2406 sheet: -1.07 (0.19), residues: 732 loop : -1.38 (0.15), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 213 TYR 0.021 0.002 TYR J 210 PHE 0.024 0.002 PHE A 169 TRP 0.012 0.002 TRP D 21 HIS 0.013 0.001 HIS I 190 Details of bonding type rmsd covalent geometry : bond 0.00484 (41998) covalent geometry : angle 0.64695 (57035) hydrogen bonds : bond 0.04830 ( 2124) hydrogen bonds : angle 5.06383 ( 6192) *********************** 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 1474 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 1231 time to evaluate : 1.495 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: A 90 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: A 256 GLN cc_start: 0.8034 (pt0) cc_final: 0.7433 (pt0) REVERT: A 257 THR cc_start: 0.8910 (m) cc_final: 0.8580 (m) REVERT: A 318 LEU cc_start: 0.9012 (mt) cc_final: 0.8752 (mp) REVERT: A 392 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7788 (t0) REVERT: A 411 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7649 (tp30) REVERT: C 90 GLU cc_start: 0.8050 (tp30) cc_final: 0.7812 (tp30) REVERT: C 121 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7876 (tpt170) REVERT: C 154 MET cc_start: 0.8735 (mmm) cc_final: 0.8427 (mmm) REVERT: C 199 ASP cc_start: 0.7491 (m-30) cc_final: 0.7288 (m-30) REVERT: C 210 TYR cc_start: 0.8406 (m-10) cc_final: 0.8070 (m-80) REVERT: C 228 ASN cc_start: 0.8590 (m-40) cc_final: 0.8149 (m110) REVERT: C 256 GLN cc_start: 0.8170 (pt0) cc_final: 0.7522 (pt0) REVERT: C 317 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8773 (mt) REVERT: C 322 ASP cc_start: 0.7738 (t0) cc_final: 0.7336 (t70) REVERT: C 377 MET cc_start: 0.8873 (tmm) cc_final: 0.8381 (tmm) REVERT: C 392 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7323 (t0) REVERT: E 50 ASN cc_start: 0.8247 (t0) cc_final: 0.7889 (t0) REVERT: E 90 GLU cc_start: 0.8112 (tp30) cc_final: 0.7740 (tp30) REVERT: E 156 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8532 (mmt-90) REVERT: E 199 ASP cc_start: 0.7294 (m-30) cc_final: 0.7064 (m-30) REVERT: E 256 GLN cc_start: 0.8087 (pt0) cc_final: 0.7379 (pt0) REVERT: E 269 LEU cc_start: 0.8980 (pp) cc_final: 0.8604 (pp) REVERT: E 336 LYS cc_start: 0.9011 (mtpm) cc_final: 0.8651 (mtpp) REVERT: E 377 MET cc_start: 0.8954 (tmm) cc_final: 0.8693 (tmm) REVERT: E 392 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7823 (t0) REVERT: J 50 ASN cc_start: 0.8484 (t0) cc_final: 0.7866 (t0) REVERT: J 103 TYR cc_start: 0.8769 (t80) cc_final: 0.8380 (t80) REVERT: J 220 GLU cc_start: 0.7333 (tp30) cc_final: 0.6953 (tp30) REVERT: J 286 LEU cc_start: 0.8686 (mt) cc_final: 0.8208 (pp) REVERT: J 293 ASN cc_start: 0.8755 (m-40) cc_final: 0.8300 (m110) REVERT: J 317 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8868 (mt) REVERT: J 326 LYS cc_start: 0.8898 (tttm) cc_final: 0.8468 (ptpt) REVERT: J 352 LYS cc_start: 0.8193 (tttp) cc_final: 0.7768 (tppt) REVERT: J 353 VAL cc_start: 0.9509 (t) cc_final: 0.9125 (p) REVERT: J 377 MET cc_start: 0.8883 (ttp) cc_final: 0.8673 (tmm) REVERT: J 392 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8126 (t0) REVERT: K 50 ASN cc_start: 0.8261 (t0) cc_final: 0.7967 (t0) REVERT: K 90 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7701 (tp30) REVERT: K 110 ILE cc_start: 0.9281 (mm) cc_final: 0.9062 (mm) REVERT: K 113 GLU cc_start: 0.8216 (mp0) cc_final: 0.7911 (mp0) REVERT: K 156 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.8029 (mmm-85) REVERT: K 199 ASP cc_start: 0.8276 (m-30) cc_final: 0.7995 (t0) REVERT: K 224 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8165 (m-80) REVERT: K 326 LYS cc_start: 0.8854 (tttm) cc_final: 0.8420 (ptpt) REVERT: K 352 LYS cc_start: 0.8152 (tttp) cc_final: 0.7682 (tppt) REVERT: K 357 TYR cc_start: 0.8272 (m-80) cc_final: 0.8048 (m-80) REVERT: K 392 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7962 (t0) REVERT: K 425 MET cc_start: 0.8729 (mmp) cc_final: 0.8487 (mmp) REVERT: L 76 ASP cc_start: 0.8754 (m-30) cc_final: 0.8313 (m-30) REVERT: L 90 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: L 103 TYR cc_start: 0.8708 (t80) cc_final: 0.8494 (t80) REVERT: L 203 MET cc_start: 0.9013 (mmm) cc_final: 0.8630 (mmm) REVERT: L 206 ASN cc_start: 0.8477 (m110) cc_final: 0.8167 (m-40) REVERT: L 210 TYR cc_start: 0.8471 (m-10) cc_final: 0.7920 (m-80) REVERT: L 322 ASP cc_start: 0.7606 (t0) cc_final: 0.7332 (t70) REVERT: L 326 LYS cc_start: 0.8843 (tttm) cc_final: 0.8342 (ptpt) REVERT: L 372 GLN cc_start: 0.7912 (mt0) cc_final: 0.7179 (pt0) REVERT: L 377 MET cc_start: 0.8962 (tmm) cc_final: 0.8570 (tmm) REVERT: L 391 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9017 (mp) REVERT: L 392 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8137 (t0) REVERT: L 425 MET cc_start: 0.8826 (mmp) cc_final: 0.8601 (mmp) REVERT: F 19 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8571 (mmmt) REVERT: F 36 TYR cc_start: 0.8325 (t80) cc_final: 0.7748 (t80) REVERT: F 112 LEU cc_start: 0.8534 (mp) cc_final: 0.8211 (tp) REVERT: F 136 THR cc_start: 0.8966 (m) cc_final: 0.8758 (p) REVERT: F 208 TYR cc_start: 0.8342 (m-10) cc_final: 0.7925 (m-10) REVERT: F 425 TYR cc_start: 0.8941 (m-80) cc_final: 0.8688 (m-80) REVERT: D 22 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7643 (tm-30) REVERT: D 26 ASP cc_start: 0.8037 (m-30) cc_final: 0.7695 (m-30) REVERT: D 46 ARG cc_start: 0.8567 (mmt-90) cc_final: 0.8182 (mmp80) REVERT: D 108 GLU cc_start: 0.8308 (tp30) cc_final: 0.7937 (tp30) REVERT: D 122 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8801 (ttmt) REVERT: D 208 TYR cc_start: 0.8247 (m-10) cc_final: 0.8033 (m-80) REVERT: D 279 GLN cc_start: 0.8428 (pm20) cc_final: 0.8036 (pt0) REVERT: D 323 MET cc_start: 0.7812 (mmm) cc_final: 0.7486 (mmm) REVERT: D 359 ARG cc_start: 0.7783 (tmm160) cc_final: 0.7565 (tmm160) REVERT: G 31 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8628 (t0) REVERT: G 106 TYR cc_start: 0.8464 (m-80) cc_final: 0.8122 (m-80) REVERT: G 116 VAL cc_start: 0.9088 (t) cc_final: 0.8862 (p) REVERT: G 121 ARG cc_start: 0.8742 (ttm110) cc_final: 0.7958 (mtm-85) REVERT: G 158 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7778 (tt0) REVERT: G 159 TYR cc_start: 0.8676 (m-80) cc_final: 0.7954 (m-80) REVERT: G 249 ASP cc_start: 0.8820 (OUTLIER) cc_final: 0.8359 (p0) REVERT: G 257 MET cc_start: 0.8535 (mmp) cc_final: 0.8129 (mmm) REVERT: G 299 MET cc_start: 0.8753 (mmp) cc_final: 0.8397 (mmp) REVERT: G 363 MET cc_start: 0.8354 (ptp) cc_final: 0.8120 (ptp) REVERT: G 388 MET cc_start: 0.8290 (mtp) cc_final: 0.7893 (mmt) REVERT: H 129 CYS cc_start: 0.8019 (t) cc_final: 0.7613 (t) REVERT: H 136 THR cc_start: 0.8685 (m) cc_final: 0.8441 (p) REVERT: H 177 ASP cc_start: 0.7645 (t70) cc_final: 0.7415 (t0) REVERT: H 249 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8211 (p0) REVERT: H 255 VAL cc_start: 0.9135 (p) cc_final: 0.8927 (p) REVERT: H 291 GLN cc_start: 0.8721 (pt0) cc_final: 0.8505 (pm20) REVERT: H 322 SER cc_start: 0.8132 (m) cc_final: 0.7860 (p) REVERT: H 388 MET cc_start: 0.8093 (mtp) cc_final: 0.7481 (mmt) REVERT: H 397 TRP cc_start: 0.8693 (m100) cc_final: 0.7770 (m-10) REVERT: H 407 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: I 26 ASP cc_start: 0.7797 (m-30) cc_final: 0.7596 (m-30) REVERT: I 31 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8227 (t0) REVERT: I 95 SER cc_start: 0.9266 (m) cc_final: 0.9017 (p) REVERT: I 158 GLU cc_start: 0.8032 (tt0) cc_final: 0.7788 (tt0) REVERT: I 198 GLU cc_start: 0.8099 (pt0) cc_final: 0.7469 (pt0) REVERT: I 200 TYR cc_start: 0.9067 (m-80) cc_final: 0.8684 (m-10) REVERT: I 209 ASP cc_start: 0.8571 (t0) cc_final: 0.8319 (t0) REVERT: I 257 MET cc_start: 0.8733 (mmp) cc_final: 0.8496 (mmm) REVERT: I 334 GLN cc_start: 0.8944 (mt0) cc_final: 0.8530 (mt0) REVERT: I 419 VAL cc_start: 0.9347 (t) cc_final: 0.9109 (p) REVERT: B 31 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: B 37 VAL cc_start: 0.8370 (OUTLIER) cc_final: 0.7970 (p) REVERT: B 46 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8388 (tpp80) REVERT: B 108 GLU cc_start: 0.8168 (tp30) cc_final: 0.7948 (tm-30) REVERT: B 121 ARG cc_start: 0.8736 (ttm110) cc_final: 0.8507 (mtm-85) REVERT: B 136 THR cc_start: 0.9038 (m) cc_final: 0.8640 (p) outliers start: 243 outliers final: 162 residues processed: 1392 average time/residue: 0.2521 time to fit residues: 576.0894 Evaluate side-chains 1337 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1154 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 PHE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 344 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 392 ASP Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 224 TYR Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 316 CYS 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 392 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS 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 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU 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 288 VAL 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 386 GLU Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain G residue 423 GLN Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 196 THR Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 347 ASN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain I residue 424 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 424 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 143 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 503 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 351 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 423 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 68 optimal weight: 0.1980 chunk 424 optimal weight: 0.7980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN L 88 HIS L 228 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 337 ASN F 424 GLN ** D 8 GLN ** 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 245 GLN G 375 GLN ** G 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 347 ASN H 375 GLN H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN I 424 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.117770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096894 restraints weight = 66579.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.100393 restraints weight = 36153.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.102858 restraints weight = 23494.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.104647 restraints weight = 17092.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105916 restraints weight = 13373.852| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 41998 Z= 0.196 Angle : 0.630 9.060 57035 Z= 0.321 Chirality : 0.045 0.172 6240 Planarity : 0.004 0.048 7411 Dihedral : 10.990 164.429 5859 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.15 % Favored : 95.79 % Rotamer: Outliers : 5.21 % Allowed : 20.69 % Favored : 74.10 % 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: -0.07 (0.12), residues: 5136 helix: 1.30 (0.11), residues: 2406 sheet: -0.93 (0.19), residues: 714 loop : -1.34 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 339 TYR 0.025 0.002 TYR J 210 PHE 0.039 0.002 PHE I 167 TRP 0.010 0.002 TRP J 407 HIS 0.009 0.001 HIS I 6 Details of bonding type rmsd covalent geometry : bond 0.00446 (41998) covalent geometry : angle 0.62986 (57035) hydrogen bonds : bond 0.04631 ( 2124) hydrogen bonds : angle 4.99262 ( 6192) *********************** 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 1455 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 1225 time to evaluate : 1.593 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 90 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: A 256 GLN cc_start: 0.7875 (pt0) cc_final: 0.7296 (pt0) REVERT: A 257 THR cc_start: 0.8993 (m) cc_final: 0.8698 (m) REVERT: A 318 LEU cc_start: 0.8917 (mt) cc_final: 0.8678 (mp) REVERT: A 392 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7760 (t0) REVERT: C 121 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7843 (tpt170) REVERT: C 154 MET cc_start: 0.8733 (mmm) cc_final: 0.8449 (mmm) REVERT: C 210 TYR cc_start: 0.8412 (m-10) cc_final: 0.8104 (m-80) REVERT: C 228 ASN cc_start: 0.8605 (m-40) cc_final: 0.8367 (m110) REVERT: C 256 GLN cc_start: 0.8236 (pt0) cc_final: 0.7596 (pt0) REVERT: C 317 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8748 (mt) REVERT: C 322 ASP cc_start: 0.7726 (t0) cc_final: 0.7322 (t70) REVERT: C 377 MET cc_start: 0.8876 (tmm) cc_final: 0.8415 (tmm) REVERT: C 392 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7599 (t0) REVERT: E 3 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6598 (mm-30) REVERT: E 50 ASN cc_start: 0.8201 (t0) cc_final: 0.7923 (t0) REVERT: E 90 GLU cc_start: 0.8145 (tp30) cc_final: 0.7728 (tp30) REVERT: E 156 ARG cc_start: 0.8844 (mmt-90) cc_final: 0.8464 (mmt-90) REVERT: E 199 ASP cc_start: 0.7381 (m-30) cc_final: 0.7166 (m-30) REVERT: E 256 GLN cc_start: 0.8110 (pt0) cc_final: 0.7420 (pt0) REVERT: E 269 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8513 (pp) REVERT: E 336 LYS cc_start: 0.9016 (mtpm) cc_final: 0.8656 (mtpp) REVERT: E 377 MET cc_start: 0.8957 (tmm) cc_final: 0.8698 (tmm) REVERT: E 392 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7869 (t0) REVERT: J 3 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5918 (mm-30) REVERT: J 243 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8628 (mtm110) REVERT: J 286 LEU cc_start: 0.8701 (mt) cc_final: 0.8204 (pp) REVERT: J 293 ASN cc_start: 0.8781 (m-40) cc_final: 0.8322 (m110) REVERT: J 300 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8413 (t0) REVERT: J 326 LYS cc_start: 0.8893 (tttm) cc_final: 0.8432 (ptpt) REVERT: J 352 LYS cc_start: 0.8174 (tttp) cc_final: 0.7747 (tppt) REVERT: J 353 VAL cc_start: 0.9506 (t) cc_final: 0.9142 (p) REVERT: J 377 MET cc_start: 0.8873 (ttp) cc_final: 0.8581 (tmm) REVERT: J 392 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8203 (t0) REVERT: K 50 ASN cc_start: 0.8304 (t0) cc_final: 0.8051 (t0) REVERT: K 90 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: K 199 ASP cc_start: 0.8334 (m-30) cc_final: 0.8084 (t0) REVERT: K 326 LYS cc_start: 0.8854 (tttm) cc_final: 0.8374 (ptpt) REVERT: K 352 LYS cc_start: 0.8128 (tttp) cc_final: 0.7570 (tppt) REVERT: K 357 TYR cc_start: 0.8258 (m-80) cc_final: 0.8030 (m-80) REVERT: K 377 MET cc_start: 0.8921 (tmm) cc_final: 0.8510 (tmm) REVERT: K 386 GLU cc_start: 0.8160 (pp20) cc_final: 0.7898 (pp20) REVERT: K 392 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.7942 (t0) REVERT: K 425 MET cc_start: 0.8781 (mmp) cc_final: 0.8522 (mmp) REVERT: L 76 ASP cc_start: 0.8736 (m-30) cc_final: 0.8247 (m-30) REVERT: L 90 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: L 103 TYR cc_start: 0.8689 (t80) cc_final: 0.8479 (t80) REVERT: L 156 ARG cc_start: 0.9014 (mmt90) cc_final: 0.8667 (mmm-85) REVERT: L 203 MET cc_start: 0.9035 (mmm) cc_final: 0.8696 (mmm) REVERT: L 206 ASN cc_start: 0.8373 (m110) cc_final: 0.7980 (m-40) REVERT: L 210 TYR cc_start: 0.8470 (m-10) cc_final: 0.7893 (m-80) REVERT: L 322 ASP cc_start: 0.7693 (t0) cc_final: 0.7413 (t70) REVERT: L 326 LYS cc_start: 0.8870 (tttm) cc_final: 0.8300 (ptpt) REVERT: L 372 GLN cc_start: 0.7956 (mt0) cc_final: 0.7219 (pt0) REVERT: L 377 MET cc_start: 0.8873 (tmm) cc_final: 0.8231 (tmm) REVERT: L 392 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8161 (t0) REVERT: F 19 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8623 (mmmt) REVERT: F 36 TYR cc_start: 0.8328 (t80) cc_final: 0.7756 (t80) REVERT: F 112 LEU cc_start: 0.8488 (mp) cc_final: 0.8244 (tp) REVERT: F 208 TYR cc_start: 0.8386 (m-10) cc_final: 0.8007 (m-10) REVERT: F 324 LYS cc_start: 0.9175 (tttp) cc_final: 0.8890 (pttp) REVERT: F 327 ASP cc_start: 0.8379 (m-30) cc_final: 0.8162 (m-30) REVERT: D 22 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7460 (tm-30) REVERT: D 26 ASP cc_start: 0.8075 (m-30) cc_final: 0.7605 (m-30) REVERT: D 86 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6758 (ttp80) REVERT: D 112 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8042 (tp) REVERT: D 122 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8796 (ttmt) REVERT: D 208 TYR cc_start: 0.8323 (m-10) cc_final: 0.8084 (m-80) REVERT: D 279 GLN cc_start: 0.8373 (pm20) cc_final: 0.8065 (pt0) REVERT: D 323 MET cc_start: 0.7769 (mmm) cc_final: 0.7510 (mmm) REVERT: D 327 ASP cc_start: 0.8203 (m-30) cc_final: 0.7927 (m-30) REVERT: D 425 TYR cc_start: 0.9082 (m-80) cc_final: 0.8863 (m-80) REVERT: G 31 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8644 (t0) REVERT: G 116 VAL cc_start: 0.9086 (t) cc_final: 0.8870 (p) REVERT: G 158 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7975 (tt0) REVERT: G 159 TYR cc_start: 0.8660 (m-80) cc_final: 0.7982 (m-80) REVERT: G 198 GLU cc_start: 0.8442 (pt0) cc_final: 0.8206 (pt0) REVERT: G 245 GLN cc_start: 0.8590 (mt0) cc_final: 0.8160 (mt0) REVERT: G 249 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8373 (p0) REVERT: G 257 MET cc_start: 0.8404 (mmp) cc_final: 0.7890 (mmm) REVERT: G 299 MET cc_start: 0.8735 (mmp) cc_final: 0.8422 (mmp) REVERT: G 363 MET cc_start: 0.8376 (ptp) cc_final: 0.8092 (ptp) REVERT: G 375 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7993 (pp30) REVERT: H 31 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8292 (t0) REVERT: H 125 GLU cc_start: 0.8154 (mp0) cc_final: 0.7801 (mp0) REVERT: H 129 CYS cc_start: 0.8101 (t) cc_final: 0.7681 (t) REVERT: H 136 THR cc_start: 0.8590 (m) cc_final: 0.8378 (p) REVERT: H 167 PHE cc_start: 0.8261 (m-80) cc_final: 0.7766 (m-80) REVERT: H 177 ASP cc_start: 0.7626 (t70) cc_final: 0.7353 (t0) REVERT: H 249 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8188 (p0) REVERT: H 291 GLN cc_start: 0.8728 (pt0) cc_final: 0.8210 (mp10) REVERT: H 297 LYS cc_start: 0.8837 (mppt) cc_final: 0.8574 (mppt) REVERT: H 322 SER cc_start: 0.8076 (m) cc_final: 0.7838 (p) REVERT: H 388 MET cc_start: 0.8070 (mtp) cc_final: 0.7406 (mmt) REVERT: H 397 TRP cc_start: 0.8630 (m100) cc_final: 0.7636 (m-10) REVERT: H 407 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: I 26 ASP cc_start: 0.7830 (m-30) cc_final: 0.7615 (m-30) REVERT: I 31 ASP cc_start: 0.8853 (t0) cc_final: 0.8279 (t0) REVERT: I 50 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: I 198 GLU cc_start: 0.8140 (pt0) cc_final: 0.7628 (pt0) REVERT: I 257 MET cc_start: 0.8734 (mmp) cc_final: 0.8455 (mmm) REVERT: I 267 MET cc_start: 0.8718 (mtt) cc_final: 0.8500 (mtm) REVERT: I 334 GLN cc_start: 0.8965 (mt0) cc_final: 0.8560 (mt0) REVERT: I 375 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8198 (pp30) REVERT: I 419 VAL cc_start: 0.9306 (t) cc_final: 0.9063 (p) REVERT: B 14 ASN cc_start: 0.8491 (m-40) cc_final: 0.8217 (m110) REVERT: B 31 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8640 (m-30) REVERT: B 37 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.7954 (p) REVERT: B 86 ARG cc_start: 0.7286 (ttp80) cc_final: 0.7039 (ttp80) REVERT: B 121 ARG cc_start: 0.8778 (ttm110) cc_final: 0.8521 (mtm-85) REVERT: B 136 THR cc_start: 0.8956 (m) cc_final: 0.8558 (p) REVERT: B 323 MET cc_start: 0.7323 (mmm) cc_final: 0.7068 (tpp) outliers start: 230 outliers final: 162 residues processed: 1380 average time/residue: 0.2478 time to fit residues: 564.2969 Evaluate side-chains 1330 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 1144 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 344 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 392 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 316 CYS 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 391 LEU Chi-restraints excluded: chain K residue 392 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 232 SER 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 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 46 ARG Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 424 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS 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 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 375 GLN Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU 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 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 144 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 168 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 310 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 483 optimal weight: 4.9990 chunk 416 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN L 50 ASN L 88 HIS L 228 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.116208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.095529 restraints weight = 67303.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.098943 restraints weight = 36673.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101360 restraints weight = 23928.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.103086 restraints weight = 17474.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104323 restraints weight = 13751.943| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 41998 Z= 0.241 Angle : 0.665 8.110 57035 Z= 0.339 Chirality : 0.046 0.192 6240 Planarity : 0.005 0.052 7411 Dihedral : 10.977 166.085 5849 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 5.80 % Allowed : 21.94 % Favored : 72.27 % 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: -0.11 (0.12), residues: 5136 helix: 1.22 (0.11), residues: 2412 sheet: -1.05 (0.19), residues: 732 loop : -1.26 (0.15), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 213 TYR 0.020 0.002 TYR L 24 PHE 0.033 0.002 PHE F 167 TRP 0.011 0.002 TRP J 407 HIS 0.007 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00548 (41998) covalent geometry : angle 0.66470 (57035) hydrogen bonds : bond 0.04846 ( 2124) hydrogen bonds : angle 5.06549 ( 6192) *********************** 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 1451 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 1195 time to evaluate : 1.557 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: A 90 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7926 (tp30) REVERT: A 199 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6631 (t70) REVERT: A 254 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 256 GLN cc_start: 0.7708 (pt0) cc_final: 0.7385 (pt0) REVERT: A 257 THR cc_start: 0.9013 (m) cc_final: 0.8699 (m) REVERT: A 392 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7544 (t0) REVERT: C 154 MET cc_start: 0.8793 (mmm) cc_final: 0.8477 (mmm) REVERT: C 210 TYR cc_start: 0.8434 (m-10) cc_final: 0.8065 (m-80) REVERT: C 228 ASN cc_start: 0.8736 (m-40) cc_final: 0.8414 (m110) REVERT: C 256 GLN cc_start: 0.8074 (pt0) cc_final: 0.7681 (pt0) REVERT: C 317 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8754 (mt) REVERT: C 322 ASP cc_start: 0.7738 (t0) cc_final: 0.7342 (t70) REVERT: C 377 MET cc_start: 0.8877 (tmm) cc_final: 0.8394 (tmm) REVERT: C 392 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7561 (t0) REVERT: E 3 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6584 (mm-30) REVERT: E 50 ASN cc_start: 0.8219 (t0) cc_final: 0.7932 (t0) REVERT: E 90 GLU cc_start: 0.8131 (tp30) cc_final: 0.7726 (tp30) REVERT: E 156 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8486 (mmt-90) REVERT: E 199 ASP cc_start: 0.7456 (m-30) cc_final: 0.7239 (m-30) REVERT: E 256 GLN cc_start: 0.8112 (pt0) cc_final: 0.7500 (pt0) REVERT: E 336 LYS cc_start: 0.9046 (mtpm) cc_final: 0.8688 (mtpp) REVERT: E 377 MET cc_start: 0.8961 (tmm) cc_final: 0.8714 (tmm) REVERT: E 392 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7871 (t0) REVERT: J 3 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6077 (mm-30) REVERT: J 103 TYR cc_start: 0.8668 (t80) cc_final: 0.8240 (t80) REVERT: J 286 LEU cc_start: 0.8589 (mt) cc_final: 0.8212 (pp) REVERT: J 293 ASN cc_start: 0.8836 (m-40) cc_final: 0.8417 (m110) REVERT: J 300 ASN cc_start: 0.8945 (t160) cc_final: 0.8642 (t0) REVERT: J 317 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8735 (mt) REVERT: J 326 LYS cc_start: 0.8917 (tttm) cc_final: 0.8487 (ptpt) REVERT: J 352 LYS cc_start: 0.8096 (tttp) cc_final: 0.7756 (tppt) REVERT: J 392 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8204 (t0) REVERT: K 90 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7802 (tp30) REVERT: K 199 ASP cc_start: 0.8331 (m-30) cc_final: 0.8084 (t0) REVERT: K 326 LYS cc_start: 0.8837 (tttm) cc_final: 0.8350 (ptpt) REVERT: K 352 LYS cc_start: 0.8023 (tttp) cc_final: 0.7451 (tppt) REVERT: K 353 VAL cc_start: 0.9448 (t) cc_final: 0.9213 (m) REVERT: K 377 MET cc_start: 0.8952 (tmm) cc_final: 0.8557 (tmm) REVERT: K 392 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7990 (t0) REVERT: L 76 ASP cc_start: 0.8753 (m-30) cc_final: 0.8277 (m-30) REVERT: L 90 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7640 (tp30) REVERT: L 103 TYR cc_start: 0.8686 (t80) cc_final: 0.8483 (t80) REVERT: L 203 MET cc_start: 0.9078 (mmm) cc_final: 0.8834 (mmm) REVERT: L 206 ASN cc_start: 0.8262 (m110) cc_final: 0.7951 (m-40) REVERT: L 210 TYR cc_start: 0.8486 (m-10) cc_final: 0.8074 (m-80) REVERT: L 322 ASP cc_start: 0.7724 (t0) cc_final: 0.7451 (t70) REVERT: L 326 LYS cc_start: 0.8850 (tttm) cc_final: 0.8125 (mttt) REVERT: L 377 MET cc_start: 0.8899 (tmm) cc_final: 0.8466 (tmm) REVERT: L 392 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.8129 (t0) REVERT: F 19 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8612 (mmmt) REVERT: F 36 TYR cc_start: 0.8319 (t80) cc_final: 0.7879 (t80) REVERT: F 112 LEU cc_start: 0.8503 (mp) cc_final: 0.8298 (tp) REVERT: F 208 TYR cc_start: 0.8396 (m-10) cc_final: 0.7991 (m-10) REVERT: F 323 MET cc_start: 0.7660 (mmm) cc_final: 0.6878 (mmm) REVERT: F 324 LYS cc_start: 0.9189 (tttp) cc_final: 0.8847 (pttp) REVERT: F 327 ASP cc_start: 0.8343 (m-30) cc_final: 0.7844 (m-30) REVERT: D 22 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7459 (tm-30) REVERT: D 26 ASP cc_start: 0.8114 (m-30) cc_final: 0.7554 (m-30) REVERT: D 86 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6892 (ttp80) REVERT: D 108 GLU cc_start: 0.8324 (tp30) cc_final: 0.8008 (tm-30) REVERT: D 122 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8825 (ttmt) REVERT: D 208 TYR cc_start: 0.8405 (m-10) cc_final: 0.8103 (m-80) REVERT: D 279 GLN cc_start: 0.8384 (pm20) cc_final: 0.8069 (pt0) REVERT: D 307 HIS cc_start: 0.8724 (m-70) cc_final: 0.8448 (m90) REVERT: D 333 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8802 (tp) REVERT: D 425 TYR cc_start: 0.9068 (m-80) cc_final: 0.8542 (m-80) REVERT: G 31 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8680 (t0) REVERT: G 116 VAL cc_start: 0.9102 (t) cc_final: 0.8894 (p) REVERT: G 158 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7967 (tt0) REVERT: G 159 TYR cc_start: 0.8705 (m-80) cc_final: 0.8034 (m-80) REVERT: G 205 GLU cc_start: 0.8233 (pt0) cc_final: 0.7982 (pt0) REVERT: G 249 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8405 (p0) REVERT: G 257 MET cc_start: 0.8403 (mmp) cc_final: 0.7906 (mmm) REVERT: G 299 MET cc_start: 0.8773 (mmp) cc_final: 0.8484 (mmp) REVERT: G 363 MET cc_start: 0.8410 (ptp) cc_final: 0.8155 (ptp) REVERT: H 31 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8303 (t0) REVERT: H 129 CYS cc_start: 0.8198 (t) cc_final: 0.7791 (t) REVERT: H 167 PHE cc_start: 0.8273 (m-80) cc_final: 0.7760 (m-80) REVERT: H 249 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8283 (p0) REVERT: H 291 GLN cc_start: 0.8713 (pt0) cc_final: 0.8227 (mp10) REVERT: H 388 MET cc_start: 0.8052 (mtp) cc_final: 0.7413 (mmt) REVERT: H 407 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: I 26 ASP cc_start: 0.7864 (m-30) cc_final: 0.7657 (m-30) REVERT: I 31 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8349 (t70) REVERT: I 198 GLU cc_start: 0.8082 (pt0) cc_final: 0.7812 (pt0) REVERT: I 257 MET cc_start: 0.8746 (mmp) cc_final: 0.8504 (mmm) REVERT: I 334 GLN cc_start: 0.8954 (mt0) cc_final: 0.8638 (mt0) REVERT: I 419 VAL cc_start: 0.9355 (t) cc_final: 0.9113 (p) REVERT: B 31 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8660 (m-30) REVERT: B 37 VAL cc_start: 0.8362 (OUTLIER) cc_final: 0.7967 (p) REVERT: B 99 ASN cc_start: 0.8997 (OUTLIER) cc_final: 0.8749 (m-40) REVERT: B 121 ARG cc_start: 0.8773 (ttm110) cc_final: 0.8477 (mtm-85) REVERT: B 136 THR cc_start: 0.8953 (m) cc_final: 0.8516 (p) REVERT: B 209 ASP cc_start: 0.8594 (t0) cc_final: 0.8253 (t0) REVERT: B 333 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8851 (tp) outliers start: 256 outliers final: 196 residues processed: 1364 average time/residue: 0.2484 time to fit residues: 558.3106 Evaluate side-chains 1346 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 1129 time to evaluate : 1.575 ------------------------------------------------------------------------------- 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 60 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 344 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 392 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 379 SER Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 200 CYS Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 290 GLU Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP 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 392 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 232 SER 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 282 TYR Chi-restraints excluded: chain L residue 287 SER Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 211 CYS Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 222 optimal weight: 5.9990 chunk 445 optimal weight: 3.9990 chunk 288 optimal weight: 30.0000 chunk 280 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 345 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 300 optimal weight: 9.9990 chunk 421 optimal weight: 8.9990 chunk 366 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN L 88 HIS ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 HIS F 424 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 334 GLN H 375 GLN H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 89 ASN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.117609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096857 restraints weight = 66729.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.100351 restraints weight = 36313.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.102803 restraints weight = 23572.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.104545 restraints weight = 17181.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.105765 restraints weight = 13494.857| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 41998 Z= 0.187 Angle : 0.631 10.031 57035 Z= 0.321 Chirality : 0.045 0.170 6240 Planarity : 0.004 0.047 7411 Dihedral : 10.801 166.942 5840 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 5.34 % Allowed : 23.09 % Favored : 71.56 % 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: 0.07 (0.12), residues: 5136 helix: 1.32 (0.11), residues: 2406 sheet: -0.95 (0.19), residues: 732 loop : -1.11 (0.15), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 339 TYR 0.026 0.001 TYR J 210 PHE 0.024 0.002 PHE F 167 TRP 0.010 0.002 TRP J 407 HIS 0.007 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00424 (41998) covalent geometry : angle 0.63149 (57035) hydrogen bonds : bond 0.04562 ( 2124) hydrogen bonds : angle 4.96412 ( 6192) *********************** 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 1457 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 1221 time to evaluate : 1.508 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 3 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6101 (mm-30) REVERT: A 90 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: A 199 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6845 (t70) REVERT: A 256 GLN cc_start: 0.7735 (pt0) cc_final: 0.7395 (pt0) REVERT: A 257 THR cc_start: 0.8990 (m) cc_final: 0.8680 (m) REVERT: C 203 MET cc_start: 0.8398 (mmm) cc_final: 0.8101 (mmm) REVERT: C 210 TYR cc_start: 0.8388 (m-10) cc_final: 0.8062 (m-80) REVERT: C 212 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8758 (mp) REVERT: C 228 ASN cc_start: 0.8712 (m-40) cc_final: 0.8386 (m110) REVERT: C 317 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8634 (mt) REVERT: C 322 ASP cc_start: 0.7741 (t0) cc_final: 0.7332 (t70) REVERT: C 377 MET cc_start: 0.8932 (tmm) cc_final: 0.8462 (tmm) REVERT: E 3 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6668 (mm-30) REVERT: E 90 GLU cc_start: 0.8121 (tp30) cc_final: 0.7716 (tp30) REVERT: E 156 ARG cc_start: 0.8892 (mmt-90) cc_final: 0.8499 (mmt-90) REVERT: E 210 TYR cc_start: 0.8493 (m-10) cc_final: 0.7960 (m-80) REVERT: E 228 ASN cc_start: 0.8650 (m-40) cc_final: 0.8298 (m110) REVERT: E 256 GLN cc_start: 0.8128 (pt0) cc_final: 0.7557 (pt0) REVERT: E 336 LYS cc_start: 0.9033 (mtpm) cc_final: 0.8671 (mtpp) REVERT: E 392 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.7994 (t0) REVERT: J 3 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6377 (mm-30) REVERT: J 103 TYR cc_start: 0.8669 (t80) cc_final: 0.8279 (t80) REVERT: J 228 ASN cc_start: 0.8901 (m-40) cc_final: 0.8675 (m-40) REVERT: J 286 LEU cc_start: 0.8533 (mt) cc_final: 0.8160 (pp) REVERT: J 293 ASN cc_start: 0.8818 (m-40) cc_final: 0.8377 (m110) REVERT: J 300 ASN cc_start: 0.8978 (OUTLIER) cc_final: 0.8564 (t0) REVERT: J 317 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8649 (mt) REVERT: J 326 LYS cc_start: 0.8948 (tttm) cc_final: 0.8434 (ptpt) REVERT: J 352 LYS cc_start: 0.8017 (tttp) cc_final: 0.7654 (tppt) REVERT: J 377 MET cc_start: 0.9036 (ttp) cc_final: 0.8291 (tmm) REVERT: J 392 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8214 (t0) REVERT: K 3 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5868 (mm-30) REVERT: K 75 ILE cc_start: 0.9084 (mm) cc_final: 0.8694 (mm) REVERT: K 90 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7773 (tp30) REVERT: K 199 ASP cc_start: 0.8351 (m-30) cc_final: 0.8082 (t0) REVERT: K 293 ASN cc_start: 0.8815 (m110) cc_final: 0.8609 (m110) REVERT: K 326 LYS cc_start: 0.8826 (tttm) cc_final: 0.8395 (ptpt) REVERT: K 352 LYS cc_start: 0.7982 (tttp) cc_final: 0.7408 (tppt) REVERT: K 353 VAL cc_start: 0.9424 (t) cc_final: 0.9195 (m) REVERT: K 377 MET cc_start: 0.8933 (tmm) cc_final: 0.8524 (tmm) REVERT: K 386 GLU cc_start: 0.8007 (pp20) cc_final: 0.7652 (pp20) REVERT: K 392 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8042 (t0) REVERT: L 76 ASP cc_start: 0.8696 (m-30) cc_final: 0.8209 (m-30) REVERT: L 90 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: L 156 ARG cc_start: 0.9070 (mmt90) cc_final: 0.8850 (mmt90) REVERT: L 203 MET cc_start: 0.9043 (mmm) cc_final: 0.8803 (mmm) REVERT: L 206 ASN cc_start: 0.8192 (m110) cc_final: 0.7942 (m-40) REVERT: L 210 TYR cc_start: 0.8466 (m-10) cc_final: 0.8010 (m-80) REVERT: L 243 ARG cc_start: 0.9024 (mtm110) cc_final: 0.8695 (mtm110) REVERT: L 322 ASP cc_start: 0.7718 (t0) cc_final: 0.7433 (t70) REVERT: L 326 LYS cc_start: 0.8847 (tttm) cc_final: 0.8090 (mttt) REVERT: L 377 MET cc_start: 0.8879 (tmm) cc_final: 0.8434 (tmm) REVERT: L 392 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8135 (t0) REVERT: F 19 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8720 (mmmt) REVERT: F 36 TYR cc_start: 0.8275 (t80) cc_final: 0.7817 (t80) REVERT: F 65 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8390 (mt) REVERT: F 112 LEU cc_start: 0.8509 (mp) cc_final: 0.8307 (tp) REVERT: F 208 TYR cc_start: 0.8338 (m-10) cc_final: 0.8023 (m-10) REVERT: F 213 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7761 (ptp-170) REVERT: F 323 MET cc_start: 0.6886 (mmm) cc_final: 0.6593 (mmm) REVERT: F 327 ASP cc_start: 0.8342 (m-30) cc_final: 0.7950 (m-30) REVERT: F 406 MET cc_start: 0.7724 (mmm) cc_final: 0.7326 (mmm) REVERT: D 22 GLU cc_start: 0.7904 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 26 ASP cc_start: 0.8122 (m-30) cc_final: 0.7509 (m-30) REVERT: D 86 ARG cc_start: 0.7188 (ttp80) cc_final: 0.6951 (ttp80) REVERT: D 108 GLU cc_start: 0.8360 (tp30) cc_final: 0.8037 (tm-30) REVERT: D 122 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8821 (ttmt) REVERT: D 208 TYR cc_start: 0.8411 (m-10) cc_final: 0.8119 (m-80) REVERT: D 209 ASP cc_start: 0.8753 (t0) cc_final: 0.8020 (t0) REVERT: D 279 GLN cc_start: 0.8369 (pm20) cc_final: 0.7986 (pt0) REVERT: D 307 HIS cc_start: 0.8728 (m-70) cc_final: 0.8435 (m90) REVERT: D 323 MET cc_start: 0.7770 (mmm) cc_final: 0.7470 (mmm) REVERT: G 11 GLN cc_start: 0.8348 (tt0) cc_final: 0.8127 (tt0) REVERT: G 31 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8660 (t0) REVERT: G 158 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7974 (tt0) REVERT: G 159 TYR cc_start: 0.8620 (m-80) cc_final: 0.7976 (m-80) REVERT: G 205 GLU cc_start: 0.8195 (pt0) cc_final: 0.7888 (pt0) REVERT: G 249 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8461 (p0) REVERT: G 257 MET cc_start: 0.8297 (mmp) cc_final: 0.7797 (mmm) REVERT: G 299 MET cc_start: 0.8711 (mmp) cc_final: 0.8418 (mmp) REVERT: G 363 MET cc_start: 0.8386 (ptp) cc_final: 0.8149 (ptp) REVERT: G 419 VAL cc_start: 0.9264 (t) cc_final: 0.9006 (p) REVERT: H 31 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8329 (t0) REVERT: H 111 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: H 125 GLU cc_start: 0.8250 (mp0) cc_final: 0.7849 (mp0) REVERT: H 129 CYS cc_start: 0.8210 (t) cc_final: 0.7805 (t) REVERT: H 136 THR cc_start: 0.8592 (m) cc_final: 0.8321 (p) REVERT: H 167 PHE cc_start: 0.8176 (m-80) cc_final: 0.7708 (m-80) REVERT: H 209 ASP cc_start: 0.8678 (t0) cc_final: 0.8280 (t0) REVERT: H 249 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8303 (p0) REVERT: H 291 GLN cc_start: 0.8705 (pt0) cc_final: 0.8205 (mp10) REVERT: H 322 SER cc_start: 0.8014 (m) cc_final: 0.7739 (p) REVERT: H 388 MET cc_start: 0.8019 (mtp) cc_final: 0.7408 (mmt) REVERT: H 407 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: I 26 ASP cc_start: 0.7876 (m-30) cc_final: 0.7651 (m-30) REVERT: I 31 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8354 (t0) REVERT: I 50 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: I 159 TYR cc_start: 0.8432 (m-80) cc_final: 0.8171 (m-80) REVERT: I 257 MET cc_start: 0.8682 (mmp) cc_final: 0.8450 (mmm) REVERT: I 291 GLN cc_start: 0.8910 (pt0) cc_final: 0.8525 (mm-40) REVERT: I 334 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8629 (mt0) REVERT: I 375 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8230 (pp30) REVERT: I 419 VAL cc_start: 0.9329 (t) cc_final: 0.9079 (p) REVERT: B 31 ASP cc_start: 0.8931 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: B 37 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 121 ARG cc_start: 0.8777 (ttm110) cc_final: 0.8477 (mtm-85) REVERT: B 136 THR cc_start: 0.8866 (m) cc_final: 0.8514 (p) REVERT: B 359 ARG cc_start: 0.7557 (ttp-170) cc_final: 0.7116 (tmm160) outliers start: 236 outliers final: 177 residues processed: 1376 average time/residue: 0.2453 time to fit residues: 557.9443 Evaluate side-chains 1360 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 1158 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 344 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 375 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 317 LEU Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 145 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 200 CYS 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 288 VAL Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 317 LEU Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP 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 392 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 238 ILE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain L residue 425 MET Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 212 PHE Chi-restraints excluded: chain D residue 234 SER Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS 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 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 334 GLN 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 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU 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 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 143 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 458 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 156 optimal weight: 0.0670 chunk 202 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 504 optimal weight: 8.9990 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN E 285 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 375 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN H 298 ASN H 334 GLN H 375 GLN ** H 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.118871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.098551 restraints weight = 66679.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.101963 restraints weight = 36096.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.104418 restraints weight = 23593.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.106166 restraints weight = 17116.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107321 restraints weight = 13377.479| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 41998 Z= 0.184 Angle : 0.642 10.865 57035 Z= 0.325 Chirality : 0.045 0.170 6240 Planarity : 0.004 0.048 7411 Dihedral : 10.708 167.670 5835 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.09 % Favored : 95.89 % Rotamer: Outliers : 5.52 % Allowed : 23.64 % Favored : 70.84 % 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: 0.08 (0.12), residues: 5136 helix: 1.35 (0.11), residues: 2406 sheet: -1.07 (0.18), residues: 774 loop : -1.06 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 339 TYR 0.028 0.002 TYR G 106 PHE 0.034 0.002 PHE F 167 TRP 0.011 0.002 TRP I 101 HIS 0.004 0.001 HIS C 61 Details of bonding type rmsd covalent geometry : bond 0.00421 (41998) covalent geometry : angle 0.64181 (57035) hydrogen bonds : bond 0.04489 ( 2124) hydrogen bonds : angle 4.94359 ( 6192) *********************** 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 1457 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 1213 time to evaluate : 1.815 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 3 GLU cc_start: 0.6561 (mm-30) cc_final: 0.6165 (mm-30) REVERT: A 33 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7499 (p0) REVERT: A 90 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7891 (tp30) REVERT: A 199 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.6768 (t70) REVERT: A 256 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: A 257 THR cc_start: 0.8968 (m) cc_final: 0.8665 (m) REVERT: C 3 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6825 (mm-30) REVERT: C 76 ASP cc_start: 0.8618 (m-30) cc_final: 0.8194 (m-30) REVERT: C 203 MET cc_start: 0.8388 (mmm) cc_final: 0.8010 (mmm) REVERT: C 210 TYR cc_start: 0.8385 (m-10) cc_final: 0.8012 (m-80) REVERT: C 212 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8738 (mp) REVERT: C 312 TYR cc_start: 0.8358 (m-80) cc_final: 0.8157 (m-80) REVERT: C 317 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8599 (mt) REVERT: C 322 ASP cc_start: 0.7724 (t0) cc_final: 0.7310 (t70) REVERT: C 377 MET cc_start: 0.8945 (tmm) cc_final: 0.8506 (tmm) REVERT: E 3 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6851 (mm-30) REVERT: E 33 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7397 (p0) REVERT: E 90 GLU cc_start: 0.8098 (tp30) cc_final: 0.7689 (tp30) REVERT: E 156 ARG cc_start: 0.8884 (mmt-90) cc_final: 0.8496 (mmt-90) REVERT: E 199 ASP cc_start: 0.7562 (m-30) cc_final: 0.7356 (t0) REVERT: E 210 TYR cc_start: 0.8492 (m-10) cc_final: 0.7961 (m-80) REVERT: E 228 ASN cc_start: 0.8660 (m-40) cc_final: 0.8291 (m110) REVERT: E 256 GLN cc_start: 0.7971 (pt0) cc_final: 0.7322 (pt0) REVERT: E 336 LYS cc_start: 0.9025 (mtpm) cc_final: 0.8670 (mtpp) REVERT: J 3 GLU cc_start: 0.6730 (mm-30) cc_final: 0.6274 (mm-30) REVERT: J 103 TYR cc_start: 0.8650 (t80) cc_final: 0.8250 (t80) REVERT: J 293 ASN cc_start: 0.8800 (m-40) cc_final: 0.8363 (m110) REVERT: J 300 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8479 (t0) REVERT: J 326 LYS cc_start: 0.8875 (tttm) cc_final: 0.8449 (ptpt) REVERT: J 352 LYS cc_start: 0.8055 (tttp) cc_final: 0.7715 (tppt) REVERT: J 377 MET cc_start: 0.9026 (ttp) cc_final: 0.8308 (tmm) REVERT: J 392 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8246 (t0) REVERT: K 3 GLU cc_start: 0.6284 (mm-30) cc_final: 0.5902 (mm-30) REVERT: K 75 ILE cc_start: 0.9056 (mm) cc_final: 0.8681 (mm) REVERT: K 90 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: K 199 ASP cc_start: 0.8374 (m-30) cc_final: 0.8107 (t0) REVERT: K 326 LYS cc_start: 0.8767 (tttm) cc_final: 0.8375 (ptpt) REVERT: K 352 LYS cc_start: 0.7970 (tttp) cc_final: 0.7421 (tppt) REVERT: K 353 VAL cc_start: 0.9414 (t) cc_final: 0.9183 (m) REVERT: K 377 MET cc_start: 0.8952 (tmm) cc_final: 0.8543 (tmm) REVERT: K 386 GLU cc_start: 0.7911 (pp20) cc_final: 0.7586 (pp20) REVERT: L 76 ASP cc_start: 0.8693 (m-30) cc_final: 0.8199 (m-30) REVERT: L 90 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: L 210 TYR cc_start: 0.8464 (m-10) cc_final: 0.8015 (m-80) REVERT: L 221 ARG cc_start: 0.7851 (ptt90) cc_final: 0.7462 (ppt90) REVERT: L 243 ARG cc_start: 0.9021 (mtm110) cc_final: 0.8675 (mtm110) REVERT: L 322 ASP cc_start: 0.7683 (t0) cc_final: 0.7401 (t70) REVERT: L 326 LYS cc_start: 0.8841 (tttm) cc_final: 0.8086 (mttt) REVERT: L 377 MET cc_start: 0.8893 (tmm) cc_final: 0.8461 (tmm) REVERT: L 392 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8030 (t0) REVERT: F 36 TYR cc_start: 0.8282 (t80) cc_final: 0.7850 (t80) REVERT: F 65 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8444 (mt) REVERT: F 108 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7999 (tm-30) REVERT: F 112 LEU cc_start: 0.8505 (mp) cc_final: 0.8302 (tp) REVERT: F 208 TYR cc_start: 0.8368 (m-10) cc_final: 0.8034 (m-10) REVERT: F 213 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7920 (ptp-170) REVERT: F 323 MET cc_start: 0.6890 (mmm) cc_final: 0.6646 (mmm) REVERT: F 327 ASP cc_start: 0.8313 (m-30) cc_final: 0.7951 (m-30) REVERT: F 406 MET cc_start: 0.7651 (mmm) cc_final: 0.7283 (mmm) REVERT: D 22 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7335 (tm-30) REVERT: D 26 ASP cc_start: 0.8079 (m-30) cc_final: 0.7432 (m-30) REVERT: D 86 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6884 (ttp80) REVERT: D 108 GLU cc_start: 0.8403 (tp30) cc_final: 0.8012 (tm-30) REVERT: D 122 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8838 (ttmt) REVERT: D 208 TYR cc_start: 0.8327 (m-10) cc_final: 0.8094 (m-80) REVERT: D 279 GLN cc_start: 0.8418 (pm20) cc_final: 0.8019 (pt0) REVERT: D 298 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8616 (t0) REVERT: D 333 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8809 (tp) REVERT: D 406 MET cc_start: 0.7750 (mmm) cc_final: 0.7475 (mmm) REVERT: D 425 TYR cc_start: 0.8993 (m-80) cc_final: 0.8614 (m-80) REVERT: G 31 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8672 (t0) REVERT: G 116 VAL cc_start: 0.9082 (t) cc_final: 0.8874 (p) REVERT: G 158 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7966 (tt0) REVERT: G 159 TYR cc_start: 0.8600 (m-80) cc_final: 0.7928 (m-80) REVERT: G 205 GLU cc_start: 0.8150 (pt0) cc_final: 0.7844 (pt0) REVERT: G 257 MET cc_start: 0.8235 (mmp) cc_final: 0.7711 (mmm) REVERT: G 299 MET cc_start: 0.8711 (mmp) cc_final: 0.8356 (mmp) REVERT: G 363 MET cc_start: 0.8389 (ptp) cc_final: 0.8156 (ptp) REVERT: G 419 VAL cc_start: 0.9279 (t) cc_final: 0.9023 (p) REVERT: H 31 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8376 (t0) REVERT: H 111 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7283 (mp0) REVERT: H 125 GLU cc_start: 0.8231 (mp0) cc_final: 0.7830 (mp0) REVERT: H 129 CYS cc_start: 0.8063 (t) cc_final: 0.7668 (t) REVERT: H 136 THR cc_start: 0.8592 (m) cc_final: 0.8359 (p) REVERT: H 167 PHE cc_start: 0.8141 (m-80) cc_final: 0.7625 (m-80) REVERT: H 249 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8317 (p0) REVERT: H 291 GLN cc_start: 0.8684 (pt0) cc_final: 0.8288 (mp10) REVERT: H 322 SER cc_start: 0.7988 (m) cc_final: 0.7716 (p) REVERT: H 388 MET cc_start: 0.8009 (mtp) cc_final: 0.7428 (mmt) REVERT: H 407 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: I 31 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8398 (t70) REVERT: I 159 TYR cc_start: 0.8464 (m-80) cc_final: 0.8219 (m-80) REVERT: I 216 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8539 (mtmm) REVERT: I 257 MET cc_start: 0.8680 (mmp) cc_final: 0.8453 (mmm) REVERT: I 334 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: I 375 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8264 (pp30) REVERT: I 419 VAL cc_start: 0.9307 (t) cc_final: 0.9055 (p) REVERT: B 31 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8645 (m-30) REVERT: B 37 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 86 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6757 (ttp80) REVERT: B 88 ASP cc_start: 0.7113 (p0) cc_final: 0.6720 (p0) REVERT: B 121 ARG cc_start: 0.8772 (ttm110) cc_final: 0.8456 (mtm-85) REVERT: B 136 THR cc_start: 0.8850 (m) cc_final: 0.8554 (p) REVERT: B 333 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8833 (tp) REVERT: B 359 ARG cc_start: 0.7461 (ttp-170) cc_final: 0.7040 (tmm160) outliers start: 244 outliers final: 183 residues processed: 1368 average time/residue: 0.2346 time to fit residues: 531.2477 Evaluate side-chains 1371 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1161 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 344 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 435 VAL Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 280 LYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 200 CYS 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 288 VAL Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP 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 L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 168 GLU Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 238 ILE 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 288 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain L residue 425 MET Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain G residue 14 ASN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS 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 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 334 GLN 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 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 333 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 178 optimal weight: 0.6980 chunk 375 optimal weight: 5.9990 chunk 373 optimal weight: 3.9990 chunk 264 optimal weight: 0.4980 chunk 405 optimal weight: 9.9990 chunk 454 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 391 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 319 optimal weight: 4.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN E 285 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN D 89 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 ASN ** 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 298 ASN H 334 GLN H 423 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 245 GLN I 375 GLN ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.118847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098246 restraints weight = 66534.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101752 restraints weight = 35940.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.104239 restraints weight = 23237.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.105968 restraints weight = 16820.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107180 restraints weight = 13180.806| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 41998 Z= 0.173 Angle : 0.644 11.092 57035 Z= 0.326 Chirality : 0.045 0.171 6240 Planarity : 0.004 0.049 7411 Dihedral : 10.615 168.220 5829 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.21 % Allowed : 24.56 % Favored : 70.23 % 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: 0.07 (0.12), residues: 5136 helix: 1.27 (0.11), residues: 2448 sheet: -0.99 (0.18), residues: 774 loop : -1.06 (0.15), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 339 TYR 0.023 0.001 TYR L 103 PHE 0.038 0.002 PHE D 20 TRP 0.013 0.002 TRP C 388 HIS 0.013 0.001 HIS I 6 Details of bonding type rmsd covalent geometry : bond 0.00393 (41998) covalent geometry : angle 0.64426 (57035) hydrogen bonds : bond 0.04433 ( 2124) hydrogen bonds : angle 4.90703 ( 6192) *********************** 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 1455 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 1225 time to evaluate : 1.492 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 3 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6240 (mm-30) REVERT: A 33 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7509 (p0) REVERT: A 90 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7935 (tp30) REVERT: A 199 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.6867 (t70) REVERT: A 256 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7443 (pt0) REVERT: A 257 THR cc_start: 0.8970 (m) cc_final: 0.8661 (m) REVERT: C 76 ASP cc_start: 0.8640 (m-30) cc_final: 0.8216 (m-30) REVERT: C 203 MET cc_start: 0.8415 (mmm) cc_final: 0.8084 (mmm) REVERT: C 210 TYR cc_start: 0.8417 (m-10) cc_final: 0.8029 (m-80) REVERT: C 212 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8711 (mp) REVERT: C 317 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8586 (mt) REVERT: C 322 ASP cc_start: 0.7714 (t0) cc_final: 0.7304 (t70) REVERT: C 377 MET cc_start: 0.8959 (tmm) cc_final: 0.8511 (tmm) REVERT: C 425 MET cc_start: 0.8945 (mmp) cc_final: 0.8721 (mmp) REVERT: E 33 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7378 (p0) REVERT: E 90 GLU cc_start: 0.8130 (tp30) cc_final: 0.7720 (tp30) REVERT: E 156 ARG cc_start: 0.8891 (mmt-90) cc_final: 0.8509 (mmt-90) REVERT: E 199 ASP cc_start: 0.7613 (m-30) cc_final: 0.7410 (t0) REVERT: E 210 TYR cc_start: 0.8461 (m-10) cc_final: 0.7935 (m-80) REVERT: E 256 GLN cc_start: 0.7978 (pt0) cc_final: 0.7320 (pt0) REVERT: E 336 LYS cc_start: 0.8998 (mtpm) cc_final: 0.8649 (mtpp) REVERT: E 392 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8008 (t0) REVERT: J 3 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6278 (mm-30) REVERT: J 103 TYR cc_start: 0.8640 (t80) cc_final: 0.8205 (t80) REVERT: J 293 ASN cc_start: 0.8798 (m-40) cc_final: 0.8366 (m110) REVERT: J 300 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8522 (t0) REVERT: J 326 LYS cc_start: 0.8885 (tttm) cc_final: 0.8456 (ptpt) REVERT: J 352 LYS cc_start: 0.8089 (tttp) cc_final: 0.7669 (tppt) REVERT: J 377 MET cc_start: 0.8897 (ttp) cc_final: 0.8506 (tmm) REVERT: J 392 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8263 (t0) REVERT: K 3 GLU cc_start: 0.6292 (mm-30) cc_final: 0.5897 (mm-30) REVERT: K 75 ILE cc_start: 0.9038 (mm) cc_final: 0.8638 (mm) REVERT: K 90 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: K 199 ASP cc_start: 0.8403 (m-30) cc_final: 0.8130 (t0) REVERT: K 322 ASP cc_start: 0.7004 (t70) cc_final: 0.6581 (p0) REVERT: K 326 LYS cc_start: 0.8789 (tttm) cc_final: 0.8365 (ptpt) REVERT: K 352 LYS cc_start: 0.7925 (tttp) cc_final: 0.7396 (tppt) REVERT: K 353 VAL cc_start: 0.9420 (t) cc_final: 0.9202 (m) REVERT: K 377 MET cc_start: 0.8929 (tmm) cc_final: 0.8506 (tmm) REVERT: K 386 GLU cc_start: 0.8014 (pp20) cc_final: 0.7680 (pp20) REVERT: L 76 ASP cc_start: 0.8671 (m-30) cc_final: 0.8165 (m-30) REVERT: L 90 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: L 169 PHE cc_start: 0.8840 (m-80) cc_final: 0.8562 (m-10) REVERT: L 203 MET cc_start: 0.9014 (mmm) cc_final: 0.8777 (mmm) REVERT: L 206 ASN cc_start: 0.8370 (m-40) cc_final: 0.8032 (m-40) REVERT: L 210 TYR cc_start: 0.8441 (m-10) cc_final: 0.8238 (m-80) REVERT: L 221 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7462 (ppt90) REVERT: L 243 ARG cc_start: 0.8979 (mtm110) cc_final: 0.8668 (mtm110) REVERT: L 322 ASP cc_start: 0.7699 (t0) cc_final: 0.7409 (t70) REVERT: L 326 LYS cc_start: 0.8854 (tttm) cc_final: 0.8094 (mttt) REVERT: L 377 MET cc_start: 0.8885 (tmm) cc_final: 0.8408 (tmm) REVERT: L 392 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8050 (t0) REVERT: F 36 TYR cc_start: 0.8240 (t80) cc_final: 0.7787 (t80) REVERT: F 46 ARG cc_start: 0.8942 (tpp80) cc_final: 0.8566 (tpp80) REVERT: F 65 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8379 (mt) REVERT: F 108 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8036 (tm-30) REVERT: F 208 TYR cc_start: 0.8387 (m-10) cc_final: 0.8046 (m-10) REVERT: F 323 MET cc_start: 0.6877 (mmm) cc_final: 0.6614 (mmm) REVERT: F 327 ASP cc_start: 0.8351 (m-30) cc_final: 0.7947 (m-30) REVERT: F 406 MET cc_start: 0.7718 (mmm) cc_final: 0.7372 (mmm) REVERT: D 22 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7345 (tm-30) REVERT: D 26 ASP cc_start: 0.8079 (m-30) cc_final: 0.7427 (m-30) REVERT: D 86 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6798 (ttp80) REVERT: D 106 TYR cc_start: 0.8525 (m-80) cc_final: 0.8317 (m-80) REVERT: D 108 GLU cc_start: 0.8371 (tp30) cc_final: 0.8004 (tm-30) REVERT: D 122 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8814 (ttmt) REVERT: D 198 GLU cc_start: 0.8404 (pt0) cc_final: 0.8098 (pt0) REVERT: D 208 TYR cc_start: 0.8367 (m-10) cc_final: 0.8123 (m-80) REVERT: D 298 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8610 (t0) REVERT: D 323 MET cc_start: 0.7741 (mmm) cc_final: 0.7163 (mmm) REVERT: D 333 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8776 (tp) REVERT: D 406 MET cc_start: 0.7771 (mmm) cc_final: 0.7518 (mmm) REVERT: D 425 TYR cc_start: 0.9027 (m-80) cc_final: 0.8662 (m-80) REVERT: G 31 ASP cc_start: 0.8956 (OUTLIER) cc_final: 0.8668 (t0) REVERT: G 116 VAL cc_start: 0.9087 (t) cc_final: 0.8870 (p) REVERT: G 158 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8022 (tt0) REVERT: G 159 TYR cc_start: 0.8571 (m-80) cc_final: 0.7910 (m-80) REVERT: G 205 GLU cc_start: 0.8161 (pt0) cc_final: 0.7830 (pt0) REVERT: G 257 MET cc_start: 0.8181 (mmp) cc_final: 0.7431 (mmm) REVERT: G 299 MET cc_start: 0.8720 (mmp) cc_final: 0.8391 (mmp) REVERT: G 320 ARG cc_start: 0.7428 (mmt180) cc_final: 0.7157 (tpm170) REVERT: G 363 MET cc_start: 0.8371 (ptp) cc_final: 0.8125 (ptp) REVERT: G 403 MET cc_start: 0.8456 (mpp) cc_final: 0.7999 (mmt) REVERT: G 419 VAL cc_start: 0.9280 (t) cc_final: 0.9008 (p) REVERT: H 31 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8389 (t0) REVERT: H 111 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: H 129 CYS cc_start: 0.8074 (t) cc_final: 0.7669 (t) REVERT: H 249 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8393 (p0) REVERT: H 291 GLN cc_start: 0.8718 (pt0) cc_final: 0.8298 (mp10) REVERT: H 322 SER cc_start: 0.7973 (m) cc_final: 0.7702 (p) REVERT: H 334 GLN cc_start: 0.8831 (mt0) cc_final: 0.8419 (mt0) REVERT: H 388 MET cc_start: 0.8028 (mtp) cc_final: 0.7419 (mmt) REVERT: H 407 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: I 31 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8387 (t0) REVERT: I 77 ARG cc_start: 0.9393 (ttm170) cc_final: 0.8742 (ttm170) REVERT: I 106 TYR cc_start: 0.8341 (m-80) cc_final: 0.7986 (m-80) REVERT: I 159 TYR cc_start: 0.8466 (m-80) cc_final: 0.8211 (m-80) REVERT: I 180 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8589 (p) REVERT: I 198 GLU cc_start: 0.8037 (pt0) cc_final: 0.7482 (pt0) REVERT: I 200 TYR cc_start: 0.8945 (m-80) cc_final: 0.8704 (m-10) REVERT: I 205 GLU cc_start: 0.8438 (pt0) cc_final: 0.8225 (pt0) REVERT: I 209 ASP cc_start: 0.8710 (t0) cc_final: 0.8315 (t0) REVERT: I 213 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7859 (ptp-170) REVERT: I 216 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8542 (mtmm) REVERT: I 257 MET cc_start: 0.8656 (mmp) cc_final: 0.8058 (mmm) REVERT: I 291 GLN cc_start: 0.8872 (pt0) cc_final: 0.8473 (mm-40) REVERT: I 322 SER cc_start: 0.7959 (m) cc_final: 0.7715 (p) REVERT: I 334 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: I 359 ARG cc_start: 0.7945 (tmm160) cc_final: 0.7744 (tmm160) REVERT: I 375 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8309 (pp30) REVERT: I 419 VAL cc_start: 0.9283 (t) cc_final: 0.9056 (p) REVERT: B 31 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8654 (m-30) REVERT: B 37 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.7951 (p) REVERT: B 121 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8480 (mtm-85) REVERT: B 136 THR cc_start: 0.8803 (m) cc_final: 0.8547 (p) REVERT: B 147 MET cc_start: 0.8303 (ttt) cc_final: 0.8023 (ttp) REVERT: B 209 ASP cc_start: 0.8558 (t0) cc_final: 0.8289 (t0) REVERT: B 213 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7823 (ptp-170) REVERT: B 333 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.8819 (tp) REVERT: B 359 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.7028 (tmm160) outliers start: 230 outliers final: 176 residues processed: 1370 average time/residue: 0.2332 time to fit residues: 527.6451 Evaluate side-chains 1378 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1172 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP 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 125 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP 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 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 287 SER Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 344 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 392 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 20 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 151 SER Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 200 CYS Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 280 LYS Chi-restraints excluded: chain J residue 287 SER Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 290 GLU Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain J residue 413 MET Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 49 PHE Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 151 SER Chi-restraints excluded: chain K residue 217 LEU 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 288 VAL Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP 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 L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 112 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 151 SER Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 200 CYS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 232 SER Chi-restraints excluded: chain L residue 237 SER Chi-restraints excluded: chain L residue 238 ILE 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 288 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain L residue 425 MET Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain F residue 31 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain D residue 298 ASN Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 211 CYS 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 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 381 ILE Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 69 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 124 CYS Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 234 SER Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 249 ASP Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 124 CYS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 178 THR Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 334 GLN Chi-restraints excluded: chain I residue 375 GLN Chi-restraints excluded: chain I residue 381 ILE Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 419 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 460 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 chunk 370 optimal weight: 0.8980 chunk 164 optimal weight: 0.0570 chunk 381 optimal weight: 0.0270 chunk 122 optimal weight: 8.9990 chunk 178 optimal weight: 0.0980 chunk 194 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 301 GLN E 216 ASN E 285 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN K 301 GLN L 50 ASN L 133 GLN F 165 ASN F 298 ASN D 134 GLN G 165 ASN H 292 GLN H 298 ASN H 375 GLN I 134 GLN I 204 ASN I 375 GLN B 165 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.124974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.104403 restraints weight = 64816.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.108062 restraints weight = 34601.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110617 restraints weight = 22168.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.112422 restraints weight = 15927.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.113729 restraints weight = 12359.250| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 41998 Z= 0.123 Angle : 0.630 11.505 57035 Z= 0.318 Chirality : 0.044 0.184 6240 Planarity : 0.004 0.075 7411 Dihedral : 10.313 165.331 5828 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.12 % Allowed : 26.94 % Favored : 69.93 % 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: 0.20 (0.12), residues: 5136 helix: 1.45 (0.11), residues: 2424 sheet: -0.95 (0.18), residues: 786 loop : -1.05 (0.15), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 339 TYR 0.018 0.001 TYR J 210 PHE 0.036 0.001 PHE D 20 TRP 0.016 0.002 TRP C 388 HIS 0.014 0.001 HIS D 6 Details of bonding type rmsd covalent geometry : bond 0.00268 (41998) covalent geometry : angle 0.62973 (57035) hydrogen bonds : bond 0.03853 ( 2124) hydrogen bonds : angle 4.77639 ( 6192) *********************** 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 1493 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 1355 time to evaluate : 1.150 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 33 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7215 (p0) REVERT: A 75 ILE cc_start: 0.8581 (mm) cc_final: 0.8329 (mm) REVERT: A 90 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7870 (tp30) REVERT: A 199 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6591 (t70) REVERT: A 243 ARG cc_start: 0.9148 (mtm110) cc_final: 0.8674 (mtm110) REVERT: A 256 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: A 257 THR cc_start: 0.8914 (m) cc_final: 0.8576 (m) REVERT: A 284 GLU cc_start: 0.6819 (pm20) cc_final: 0.6604 (tp30) REVERT: A 377 MET cc_start: 0.8698 (tmm) cc_final: 0.8362 (tmm) REVERT: C 3 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6788 (mm-30) REVERT: C 76 ASP cc_start: 0.8535 (m-30) cc_final: 0.8089 (m-30) REVERT: C 153 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8716 (mp) REVERT: C 203 MET cc_start: 0.8398 (mmm) cc_final: 0.8059 (mmm) REVERT: C 210 TYR cc_start: 0.8331 (m-10) cc_final: 0.7886 (m-80) REVERT: C 212 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8767 (mp) REVERT: C 233 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8776 (mm-40) REVERT: C 317 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8526 (mt) REVERT: C 322 ASP cc_start: 0.7649 (t0) cc_final: 0.7274 (t70) REVERT: C 377 MET cc_start: 0.8893 (tmm) cc_final: 0.8449 (tmm) REVERT: E 3 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6297 (mm-30) REVERT: E 33 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7378 (p0) REVERT: E 90 GLU cc_start: 0.8050 (tp30) cc_final: 0.7642 (tp30) REVERT: E 156 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8469 (mmt-90) REVERT: E 199 ASP cc_start: 0.7377 (m-30) cc_final: 0.7126 (t0) REVERT: E 210 TYR cc_start: 0.8368 (m-10) cc_final: 0.7879 (m-80) REVERT: E 237 SER cc_start: 0.9001 (m) cc_final: 0.8681 (t) REVERT: E 256 GLN cc_start: 0.7906 (pt0) cc_final: 0.7210 (pt0) REVERT: E 336 LYS cc_start: 0.8952 (mtpm) cc_final: 0.8628 (mtpp) REVERT: E 392 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7918 (t0) REVERT: J 3 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6185 (mm-30) REVERT: J 103 TYR cc_start: 0.8575 (t80) cc_final: 0.8158 (t80) REVERT: J 293 ASN cc_start: 0.8743 (m-40) cc_final: 0.8285 (m110) REVERT: J 300 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8431 (t0) REVERT: J 326 LYS cc_start: 0.8888 (tttm) cc_final: 0.8447 (ptpt) REVERT: J 352 LYS cc_start: 0.7983 (tttp) cc_final: 0.7618 (tppt) REVERT: J 377 MET cc_start: 0.8819 (ttp) cc_final: 0.8527 (tmm) REVERT: J 392 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8323 (t0) REVERT: J 425 MET cc_start: 0.8539 (mmp) cc_final: 0.8154 (tpp) REVERT: K 3 GLU cc_start: 0.6341 (mm-30) cc_final: 0.5955 (mm-30) REVERT: K 75 ILE cc_start: 0.8851 (mm) cc_final: 0.8480 (mm) REVERT: K 90 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7724 (tp30) REVERT: K 199 ASP cc_start: 0.8271 (m-30) cc_final: 0.7961 (t0) REVERT: K 322 ASP cc_start: 0.7009 (t70) cc_final: 0.6631 (p0) REVERT: K 326 LYS cc_start: 0.8776 (tttm) cc_final: 0.8336 (ptpt) REVERT: K 352 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7386 (tppt) REVERT: K 353 VAL cc_start: 0.9385 (t) cc_final: 0.9173 (m) REVERT: K 377 MET cc_start: 0.8923 (tmm) cc_final: 0.8506 (tmm) REVERT: L 75 ILE cc_start: 0.8968 (mm) cc_final: 0.8703 (mm) REVERT: L 76 ASP cc_start: 0.8657 (m-30) cc_final: 0.8177 (m-30) REVERT: L 90 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: L 169 PHE cc_start: 0.8729 (m-80) cc_final: 0.8507 (m-80) REVERT: L 203 MET cc_start: 0.8920 (mmm) cc_final: 0.8667 (mmm) REVERT: L 210 TYR cc_start: 0.8580 (m-10) cc_final: 0.8196 (m-80) REVERT: L 221 ARG cc_start: 0.7805 (ptt90) cc_final: 0.7552 (ppt90) REVERT: L 243 ARG cc_start: 0.8929 (mtm110) cc_final: 0.8587 (mtm110) REVERT: L 322 ASP cc_start: 0.7634 (t0) cc_final: 0.7347 (t70) REVERT: L 326 LYS cc_start: 0.8874 (tttm) cc_final: 0.8072 (mttt) REVERT: L 377 MET cc_start: 0.8903 (tmm) cc_final: 0.8426 (tmm) REVERT: L 392 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.7722 (t0) REVERT: L 402 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8299 (ttm110) REVERT: F 36 TYR cc_start: 0.8158 (t80) cc_final: 0.7656 (t80) REVERT: F 65 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8346 (mt) REVERT: F 108 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8025 (tm-30) REVERT: F 121 ARG cc_start: 0.8946 (ttm110) cc_final: 0.8640 (mtm-85) REVERT: F 147 MET cc_start: 0.8478 (ttp) cc_final: 0.8276 (ttp) REVERT: F 209 ASP cc_start: 0.8473 (t0) cc_final: 0.6891 (t0) REVERT: F 213 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7669 (ptp-170) REVERT: F 323 MET cc_start: 0.6699 (mmm) cc_final: 0.6465 (mmm) REVERT: F 327 ASP cc_start: 0.8302 (m-30) cc_final: 0.7920 (m-30) REVERT: F 423 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8635 (pp30) REVERT: D 22 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7319 (tm-30) REVERT: D 26 ASP cc_start: 0.7941 (m-30) cc_final: 0.7323 (m-30) REVERT: D 77 ARG cc_start: 0.9108 (ttm170) cc_final: 0.8865 (mtm-85) REVERT: D 122 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8804 (ttpt) REVERT: D 257 MET cc_start: 0.8169 (mmm) cc_final: 0.7778 (mmm) REVERT: D 315 THR cc_start: 0.9045 (m) cc_final: 0.8821 (p) REVERT: D 406 MET cc_start: 0.7711 (mmm) cc_final: 0.7481 (mmm) REVERT: G 31 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8610 (t70) REVERT: G 121 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8048 (mtm-85) REVERT: G 158 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7801 (tt0) REVERT: G 159 TYR cc_start: 0.8428 (m-80) cc_final: 0.7645 (m-80) REVERT: G 180 VAL cc_start: 0.9047 (m) cc_final: 0.8658 (p) REVERT: G 196 THR cc_start: 0.7801 (m) cc_final: 0.7542 (m) REVERT: G 249 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8286 (p0) REVERT: G 257 MET cc_start: 0.8246 (mmp) cc_final: 0.7711 (mmt) REVERT: G 299 MET cc_start: 0.8659 (mmp) cc_final: 0.8450 (mmp) REVERT: G 363 MET cc_start: 0.8327 (ptp) cc_final: 0.8106 (ptp) REVERT: G 403 MET cc_start: 0.8334 (mpp) cc_final: 0.7903 (mmt) REVERT: G 407 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: G 419 VAL cc_start: 0.9234 (t) cc_final: 0.8993 (p) REVERT: H 31 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8369 (t0) REVERT: H 129 CYS cc_start: 0.8050 (t) cc_final: 0.7742 (t) REVERT: H 147 MET cc_start: 0.8470 (ttm) cc_final: 0.8216 (ttm) REVERT: H 167 PHE cc_start: 0.7994 (m-80) cc_final: 0.7622 (m-80) REVERT: H 213 ARG cc_start: 0.8370 (ttp-110) cc_final: 0.8021 (ptp-170) REVERT: H 291 GLN cc_start: 0.8645 (pt0) cc_final: 0.8221 (mp10) REVERT: H 299 MET cc_start: 0.8622 (mmp) cc_final: 0.8392 (mmp) REVERT: H 334 GLN cc_start: 0.8772 (mt0) cc_final: 0.8323 (mt0) REVERT: H 374 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8335 (tt) REVERT: H 388 MET cc_start: 0.7897 (mtp) cc_final: 0.7384 (mmt) REVERT: H 407 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: I 31 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8313 (t0) REVERT: I 77 ARG cc_start: 0.9337 (ttm170) cc_final: 0.8778 (ttm170) REVERT: I 180 VAL cc_start: 0.9011 (m) cc_final: 0.8503 (p) REVERT: I 198 GLU cc_start: 0.8098 (pt0) cc_final: 0.7585 (pt0) REVERT: I 200 TYR cc_start: 0.8861 (m-80) cc_final: 0.8654 (m-10) REVERT: I 205 GLU cc_start: 0.8391 (pt0) cc_final: 0.8176 (pt0) REVERT: I 216 LYS cc_start: 0.8763 (mmtp) cc_final: 0.8513 (mtmm) REVERT: I 257 MET cc_start: 0.8626 (mmp) cc_final: 0.8025 (mmm) REVERT: I 291 GLN cc_start: 0.8813 (pt0) cc_final: 0.8504 (mm-40) REVERT: I 334 GLN cc_start: 0.8889 (mt0) cc_final: 0.8556 (mt0) REVERT: I 347 ASN cc_start: 0.7703 (m110) cc_final: 0.7485 (t0) REVERT: I 406 MET cc_start: 0.8236 (mmm) cc_final: 0.7916 (mmm) REVERT: I 419 VAL cc_start: 0.9251 (t) cc_final: 0.8976 (p) REVERT: B 24 ILE cc_start: 0.8187 (mm) cc_final: 0.7565 (mt) REVERT: B 31 ASP cc_start: 0.8955 (m-30) cc_final: 0.8729 (m-30) REVERT: B 37 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8154 (p) REVERT: B 121 ARG cc_start: 0.8721 (ttm110) cc_final: 0.8457 (mtm-85) REVERT: B 147 MET cc_start: 0.7945 (ttt) cc_final: 0.7688 (ttp) REVERT: B 167 PHE cc_start: 0.8201 (m-80) cc_final: 0.7590 (m-10) REVERT: B 255 VAL cc_start: 0.9091 (p) cc_final: 0.8865 (p) REVERT: B 329 GLN cc_start: 0.9191 (mm110) cc_final: 0.8929 (mm-40) REVERT: B 359 ARG cc_start: 0.7347 (ttp-170) cc_final: 0.6938 (tmm160) outliers start: 138 outliers final: 84 residues processed: 1441 average time/residue: 0.2387 time to fit residues: 565.2246 Evaluate side-chains 1328 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1218 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 145 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 280 LYS Chi-restraints excluded: chain J residue 300 ASN Chi-restraints excluded: chain J residue 316 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 352 LYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 298 ASN Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 375 GLN Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain H residue 423 GLN Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 83 HIS Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 119 optimal weight: 0.0010 chunk 275 optimal weight: 0.7980 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: 10.0000 chunk 276 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 375 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN E 133 GLN E 216 ASN E 285 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN L 88 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN F 165 ASN F 298 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 ASN D 298 ASN G 134 GLN G 165 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS H 89 ASN H 298 ASN H 423 GLN H 424 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 292 GLN I 298 ASN I 423 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.121945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.101581 restraints weight = 65854.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105133 restraints weight = 35420.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107641 restraints weight = 22795.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109419 restraints weight = 16422.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.110676 restraints weight = 12782.877| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 41998 Z= 0.162 Angle : 0.682 17.193 57035 Z= 0.342 Chirality : 0.045 0.218 6240 Planarity : 0.005 0.083 7411 Dihedral : 10.316 165.332 5818 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.81 % Allowed : 28.41 % Favored : 68.78 % 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: 0.18 (0.12), residues: 5136 helix: 1.36 (0.11), residues: 2460 sheet: -0.80 (0.19), residues: 774 loop : -1.07 (0.15), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG G 282 TYR 0.024 0.001 TYR A 161 PHE 0.048 0.002 PHE H 20 TRP 0.015 0.002 TRP C 388 HIS 0.014 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00373 (41998) covalent geometry : angle 0.68159 (57035) hydrogen bonds : bond 0.04167 ( 2124) hydrogen bonds : angle 4.81049 ( 6192) ********************** 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 1357 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1233 time to evaluate : 1.281 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 3 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6424 (mm-30) REVERT: A 33 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7267 (p0) REVERT: A 75 ILE cc_start: 0.8711 (mm) cc_final: 0.8416 (mm) REVERT: A 154 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8572 (mmt) REVERT: A 199 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6864 (t70) REVERT: A 243 ARG cc_start: 0.9128 (mtm110) cc_final: 0.8655 (mtm110) REVERT: A 256 GLN cc_start: 0.7664 (pt0) cc_final: 0.7378 (pt0) REVERT: A 257 THR cc_start: 0.8834 (m) cc_final: 0.8549 (m) REVERT: C 3 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6627 (mm-30) REVERT: C 31 GLN cc_start: 0.8493 (mm-40) cc_final: 0.7852 (mp10) REVERT: C 76 ASP cc_start: 0.8574 (m-30) cc_final: 0.8155 (m-30) REVERT: C 203 MET cc_start: 0.8429 (mmm) cc_final: 0.8116 (mmm) REVERT: C 210 TYR cc_start: 0.8393 (m-10) cc_final: 0.7894 (m-80) REVERT: C 212 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8744 (mp) REVERT: C 322 ASP cc_start: 0.7791 (t0) cc_final: 0.7348 (t70) REVERT: C 377 MET cc_start: 0.8917 (tmm) cc_final: 0.8503 (tmm) REVERT: E 3 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6315 (mm-30) REVERT: E 33 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7452 (p0) REVERT: E 90 GLU cc_start: 0.8077 (tp30) cc_final: 0.7661 (tp30) REVERT: E 156 ARG cc_start: 0.8861 (mmt-90) cc_final: 0.8477 (mmt-90) REVERT: E 199 ASP cc_start: 0.7494 (m-30) cc_final: 0.7157 (t0) REVERT: E 228 ASN cc_start: 0.8657 (m-40) cc_final: 0.8357 (m110) REVERT: E 256 GLN cc_start: 0.7956 (pt0) cc_final: 0.7275 (pt0) REVERT: E 293 ASN cc_start: 0.8687 (m-40) cc_final: 0.8363 (m110) REVERT: E 336 LYS cc_start: 0.8980 (mtpm) cc_final: 0.8635 (mtpp) REVERT: E 413 MET cc_start: 0.7125 (mmm) cc_final: 0.6624 (mpp) REVERT: J 3 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6291 (mm-30) REVERT: J 71 GLU cc_start: 0.7438 (pt0) cc_final: 0.7230 (tt0) REVERT: J 103 TYR cc_start: 0.8570 (t80) cc_final: 0.8130 (t80) REVERT: J 293 ASN cc_start: 0.8765 (m-40) cc_final: 0.8323 (m110) REVERT: J 300 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8487 (t0) REVERT: J 322 ASP cc_start: 0.7405 (t70) cc_final: 0.6942 (p0) REVERT: J 326 LYS cc_start: 0.8900 (tttm) cc_final: 0.8436 (ptpt) REVERT: J 352 LYS cc_start: 0.8056 (tttp) cc_final: 0.7649 (tppt) REVERT: J 392 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8342 (t0) REVERT: K 3 GLU cc_start: 0.6291 (mm-30) cc_final: 0.5930 (mm-30) REVERT: K 75 ILE cc_start: 0.8966 (mm) cc_final: 0.8587 (mm) REVERT: K 90 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7773 (tp30) REVERT: K 199 ASP cc_start: 0.8318 (m-30) cc_final: 0.8020 (t0) REVERT: K 326 LYS cc_start: 0.8785 (tttm) cc_final: 0.8360 (ptpt) REVERT: K 352 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7362 (tppt) REVERT: K 377 MET cc_start: 0.8923 (tmm) cc_final: 0.8490 (tmm) REVERT: L 75 ILE cc_start: 0.9028 (mm) cc_final: 0.8774 (mm) REVERT: L 76 ASP cc_start: 0.8719 (m-30) cc_final: 0.8264 (m-30) REVERT: L 90 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7514 (tp30) REVERT: L 169 PHE cc_start: 0.8818 (m-80) cc_final: 0.8530 (m-10) REVERT: L 203 MET cc_start: 0.8948 (mmm) cc_final: 0.8719 (mmm) REVERT: L 210 TYR cc_start: 0.8612 (m-10) cc_final: 0.8239 (m-80) REVERT: L 221 ARG cc_start: 0.7812 (ptt90) cc_final: 0.7515 (ppt90) REVERT: L 243 ARG cc_start: 0.8951 (mtm110) cc_final: 0.8646 (mtm110) REVERT: L 322 ASP cc_start: 0.7662 (t0) cc_final: 0.7382 (t70) REVERT: L 326 LYS cc_start: 0.8881 (tttm) cc_final: 0.8083 (mttt) REVERT: L 377 MET cc_start: 0.8915 (tmm) cc_final: 0.8418 (tmm) REVERT: L 392 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8302 (t0) REVERT: L 402 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8406 (ttm110) REVERT: F 36 TYR cc_start: 0.8202 (t80) cc_final: 0.7717 (t80) REVERT: F 108 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8062 (tm-30) REVERT: F 121 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8641 (mtm-85) REVERT: F 147 MET cc_start: 0.8491 (ttp) cc_final: 0.8271 (ttp) REVERT: F 209 ASP cc_start: 0.8418 (t0) cc_final: 0.6812 (t0) REVERT: F 213 ARG cc_start: 0.8095 (ptp-170) cc_final: 0.7713 (ptp-170) REVERT: F 320 ARG cc_start: 0.7289 (tpp-160) cc_final: 0.7025 (mmm160) REVERT: F 327 ASP cc_start: 0.8336 (m-30) cc_final: 0.8130 (m-30) REVERT: D 22 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7314 (tm-30) REVERT: D 26 ASP cc_start: 0.7956 (m-30) cc_final: 0.7355 (m-30) REVERT: D 108 GLU cc_start: 0.8378 (tp30) cc_final: 0.8097 (tm-30) REVERT: D 257 MET cc_start: 0.8225 (mmm) cc_final: 0.7678 (mmm) REVERT: D 406 MET cc_start: 0.7704 (mmm) cc_final: 0.7464 (mmm) REVERT: D 423 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8415 (pp30) REVERT: G 31 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8673 (t70) REVERT: G 158 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8067 (tt0) REVERT: G 159 TYR cc_start: 0.8493 (m-80) cc_final: 0.7708 (m-80) REVERT: G 167 PHE cc_start: 0.8162 (m-80) cc_final: 0.7864 (m-10) REVERT: G 180 VAL cc_start: 0.9079 (m) cc_final: 0.8746 (p) REVERT: G 249 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8476 (p0) REVERT: G 299 MET cc_start: 0.8692 (mmp) cc_final: 0.8388 (mmp) REVERT: G 306 ARG cc_start: 0.9244 (mpp80) cc_final: 0.9020 (mpp80) REVERT: G 363 MET cc_start: 0.8369 (ptp) cc_final: 0.8163 (ptp) REVERT: G 407 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: G 419 VAL cc_start: 0.9293 (t) cc_final: 0.9011 (p) REVERT: H 31 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8402 (t0) REVERT: H 73 MET cc_start: 0.8254 (mmt) cc_final: 0.8016 (mmm) REVERT: H 129 CYS cc_start: 0.8118 (t) cc_final: 0.7772 (t) REVERT: H 209 ASP cc_start: 0.8655 (t0) cc_final: 0.8288 (t0) REVERT: H 213 ARG cc_start: 0.8387 (ttp-110) cc_final: 0.7988 (ptp-170) REVERT: H 282 ARG cc_start: 0.7787 (tpt170) cc_final: 0.7425 (tpt90) REVERT: H 291 GLN cc_start: 0.8686 (pt0) cc_final: 0.8218 (mp10) REVERT: H 374 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8361 (tt) REVERT: H 388 MET cc_start: 0.7917 (mtp) cc_final: 0.7337 (mmt) REVERT: H 403 MET cc_start: 0.8120 (mpp) cc_final: 0.7677 (mmm) REVERT: H 407 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: I 31 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8344 (t0) REVERT: I 73 MET cc_start: 0.8805 (mpp) cc_final: 0.8472 (mmm) REVERT: I 77 ARG cc_start: 0.9327 (ttm170) cc_final: 0.8833 (ttm170) REVERT: I 106 TYR cc_start: 0.8355 (m-80) cc_final: 0.8155 (m-80) REVERT: I 198 GLU cc_start: 0.8110 (pt0) cc_final: 0.7574 (pt0) REVERT: I 200 TYR cc_start: 0.8904 (m-80) cc_final: 0.8620 (m-10) REVERT: I 205 GLU cc_start: 0.8391 (pt0) cc_final: 0.8125 (pt0) REVERT: I 216 LYS cc_start: 0.8760 (mmtp) cc_final: 0.8507 (mtmm) REVERT: I 257 MET cc_start: 0.8651 (mmp) cc_final: 0.8052 (mmm) REVERT: I 291 GLN cc_start: 0.8841 (pt0) cc_final: 0.8474 (mm-40) REVERT: I 300 MET cc_start: 0.9086 (tpp) cc_final: 0.8561 (tpp) REVERT: I 334 GLN cc_start: 0.8896 (mt0) cc_final: 0.8539 (mt0) REVERT: I 419 VAL cc_start: 0.9308 (t) cc_final: 0.9089 (p) REVERT: B 121 ARG cc_start: 0.8727 (ttm110) cc_final: 0.8450 (mtm-85) REVERT: B 359 ARG cc_start: 0.7375 (ttp-170) cc_final: 0.6962 (tmm160) outliers start: 124 outliers final: 87 residues processed: 1306 average time/residue: 0.2409 time to fit residues: 516.3405 Evaluate side-chains 1296 residues out of total 4428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1190 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 379 SER Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain J residue 4 CYS Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 145 THR 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 316 CYS Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 392 ASP Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 316 CYS Chi-restraints excluded: chain K residue 352 LYS Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 379 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 90 GLU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 145 THR Chi-restraints excluded: chain L residue 198 SER Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 316 CYS Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 391 LEU Chi-restraints excluded: chain L residue 392 ASP Chi-restraints excluded: chain L residue 402 ARG Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 249 ASP Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 249 ASP Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain G residue 178 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 362 LYS Chi-restraints excluded: chain G residue 407 GLU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain H residue 26 ASP Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 178 THR Chi-restraints excluded: chain H residue 240 LEU Chi-restraints excluded: chain H residue 374 ILE Chi-restraints excluded: chain H residue 407 GLU Chi-restraints excluded: chain I residue 31 ASP Chi-restraints excluded: chain I residue 125 GLU Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 152 ILE Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 423 GLN Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 124 CYS Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 336 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 435 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 410 optimal weight: 7.9990 chunk 496 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN E 186 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN E 285 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 334 GLN H 375 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 ASN ** I 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.101557 restraints weight = 66046.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105180 restraints weight = 35468.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107700 restraints weight = 22754.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109487 restraints weight = 16419.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.110711 restraints weight = 12794.447| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 41998 Z= 0.151 Angle : 0.674 16.701 57035 Z= 0.339 Chirality : 0.045 0.361 6240 Planarity : 0.005 0.085 7411 Dihedral : 10.298 166.243 5813 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.88 % Allowed : 28.50 % Favored : 68.62 % 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: 1.39 (0.11), residues: 2430 sheet: -0.86 (0.18), residues: 798 loop : -1.02 (0.15), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 282 TYR 0.028 0.001 TYR I 159 PHE 0.048 0.002 PHE H 20 TRP 0.024 0.002 TRP D 397 HIS 0.013 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00347 (41998) covalent geometry : angle 0.67397 (57035) hydrogen bonds : bond 0.04143 ( 2124) hydrogen bonds : angle 4.78498 ( 6192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10257.72 seconds wall clock time: 176 minutes 56.82 seconds (10616.82 seconds total)