Starting phenix.real_space_refine on Sat Jun 28 19:10:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dqv_47116/06_2025/9dqv_47116.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dqv_47116/06_2025/9dqv_47116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dqv_47116/06_2025/9dqv_47116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dqv_47116/06_2025/9dqv_47116.map" model { file = "/net/cci-nas-00/data/ceres_data/9dqv_47116/06_2025/9dqv_47116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dqv_47116/06_2025/9dqv_47116.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.011 sd= 0.070 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: 4 Type Number sf(0) Gaussians S 199 5.16 5 C 21348 2.51 5 N 5765 2.21 5 O 6389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33701 Number of models: 1 Model: "" Number of chains: 24 Chain: "D" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3277 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 406} Chain: "E" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3148 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 26, 'TRANS': 373} Chain breaks: 1 Chain: "F" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "G" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3277 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 406} Chain: "H" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3148 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 26, 'TRANS': 373} Chain breaks: 1 Chain: "I" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "J" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3277 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 406} Chain: "K" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3148 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 26, 'TRANS': 373} Chain breaks: 1 Chain: "L" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1214 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 148} Chain: "M" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain breaks: 1 Chain: "N" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain breaks: 1 Chain: "O" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain breaks: 1 Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3277 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 406} Chain: "B" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3152 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 26, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1191 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain breaks: 1 Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 18.68, per 1000 atoms: 0.55 Number of scatterers: 33701 At special positions: 0 Unit cell: (152.64, 195.04, 189.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 199 16.00 O 6389 8.00 N 5765 7.00 C 21348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.04 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 16 " - pdb=" SG CYS E 124 " distance=2.04 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 91 " - pdb=" SG CYS E 105 " distance=2.03 Simple disulfide: pdb=" SG CYS E 152 " - pdb=" SG CYS E 266 " distance=2.04 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 226 " distance=2.03 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.04 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.02 Simple disulfide: pdb=" SG CYS H 16 " - pdb=" SG CYS H 124 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 25 " distance=2.03 Simple disulfide: pdb=" SG CYS H 91 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 266 " distance=2.04 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 226 " distance=2.03 Simple disulfide: pdb=" SG CYS H 203 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.04 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 68 " - pdb=" SG CYS J 78 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.04 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 124 " distance=2.04 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 25 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 266 " distance=2.04 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 226 " distance=2.04 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 67 " - pdb=" SG CYS M 73 " distance=2.03 Simple disulfide: pdb=" SG CYS N 67 " - pdb=" SG CYS N 73 " distance=2.03 Simple disulfide: pdb=" SG CYS O 67 " - pdb=" SG CYS O 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.02 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS P 67 " - pdb=" SG CYS P 73 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 139 " " NAG A 502 " - " ASN A 245 " " NAG B 501 " - " ASN B 196 " " NAG B 502 " - " ASN B 318 " " NAG D 501 " - " ASN D 139 " " NAG D 502 " - " ASN D 245 " " NAG E 501 " - " ASN E 196 " " NAG E 502 " - " ASN E 318 " " NAG G 501 " - " ASN G 139 " " NAG G 502 " - " ASN G 245 " " NAG H 501 " - " ASN H 196 " " NAG H 502 " - " ASN H 318 " " NAG J 501 " - " ASN J 139 " " NAG J 502 " - " ASN J 245 " " NAG K 501 " - " ASN K 196 " " NAG K 502 " - " ASN K 318 " Time building additional restraints: 7.20 Conformation dependent library (CDL) restraints added in 4.2 seconds 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 103 sheets defined 12.3% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.825A pdb=" N VAL D 402 " --> pdb=" O PHE D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 433 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.501A pdb=" N TYR E 179 " --> pdb=" O TYR E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 363 removed outlier: 3.678A pdb=" N ILE E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 402 Proline residue: E 399 - end of helix removed outlier: 3.604A pdb=" N LEU E 402 " --> pdb=" O THR E 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 11 Processing helix chain 'F' and resid 47 through 51 Processing helix chain 'G' and resid 96 through 99 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.731A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 403 through 433 Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 351 through 363 Processing helix chain 'H' and resid 363 through 398 Processing helix chain 'H' and resid 398 through 403 removed outlier: 3.890A pdb=" N ALA H 403 " --> pdb=" O PRO H 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 11 removed outlier: 3.561A pdb=" N GLU I 11 " --> pdb=" O CYS I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 11' Processing helix chain 'J' and resid 111 through 116 removed outlier: 4.299A pdb=" N THR J 115 " --> pdb=" O PRO J 112 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE J 116 " --> pdb=" O ASP J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 140 removed outlier: 3.661A pdb=" N ASN J 139 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 246 removed outlier: 3.799A pdb=" N ASN J 246 " --> pdb=" O MET J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 259 removed outlier: 3.869A pdb=" N GLY J 258 " --> pdb=" O ALA J 255 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N CYS J 259 " --> pdb=" O PRO J 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 255 through 259' Processing helix chain 'J' and resid 403 through 434 Processing helix chain 'K' and resid 5 through 9 removed outlier: 4.123A pdb=" N LEU K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 180 removed outlier: 4.005A pdb=" N TYR K 179 " --> pdb=" O TYR K 176 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU K 180 " --> pdb=" O LYS K 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 176 through 180' Processing helix chain 'K' and resid 191 through 195 removed outlier: 3.818A pdb=" N GLY K 194 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 226 removed outlier: 4.200A pdb=" N GLN K 225 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS K 226 " --> pdb=" O ALA K 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 222 through 226' Processing helix chain 'K' and resid 351 through 363 Processing helix chain 'K' and resid 363 through 403 Proline residue: K 399 - end of helix Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 47 through 51 Processing helix chain 'M' and resid 19 through 24 Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'N' and resid 19 through 24 Processing helix chain 'N' and resid 26 through 30 removed outlier: 3.598A pdb=" N LYS N 29 " --> pdb=" O ASP N 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 24 Processing helix chain 'O' and resid 26 through 30 removed outlier: 3.869A pdb=" N LYS O 29 " --> pdb=" O ASP O 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 removed outlier: 4.393A pdb=" N THR A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.912A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 434 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.795A pdb=" N LEU B 8 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 178 No H-bonds generated for 'chain 'B' and resid 176 through 178' Processing helix chain 'B' and resid 351 through 363 removed outlier: 3.557A pdb=" N ILE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 398 Processing helix chain 'C' and resid 7 through 11 Processing helix chain 'P' and resid 19 through 23 Processing helix chain 'P' and resid 62 through 67 Processing sheet with id=AA1, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.889A pdb=" N LYS D 160 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 15 through 20 removed outlier: 7.694A pdb=" N GLU D 30 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR D 137 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR D 32 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE D 135 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL D 34 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU D 133 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER D 36 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 131 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 38 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU D 129 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA D 127 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR D 42 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N HIS D 125 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS D 44 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LYS D 123 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.646A pdb=" N LYS D 123 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS D 44 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N HIS D 125 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR D 42 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA D 127 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU D 129 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU D 38 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL D 131 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER D 36 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU D 133 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL D 34 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE D 135 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N THR D 32 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR D 137 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLU D 30 " --> pdb=" O TYR D 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AA5, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.840A pdb=" N MET D 88 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AA8, first strand: chain 'D' and resid 296 through 304 removed outlier: 4.287A pdb=" N GLU D 298 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 315 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'D' and resid 365 through 367 Processing sheet with id=AB2, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'D' and resid 387 through 388 removed outlier: 7.299A pdb=" N LEU E 285 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHE E 319 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU E 287 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ARG E 317 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ALA E 289 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR E 315 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG E 291 " --> pdb=" O GLY E 313 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLY E 313 " --> pdb=" O ARG E 291 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AB5, first strand: chain 'E' and resid 31 through 35 removed outlier: 8.627A pdb=" N ILE E 31 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER E 48 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN E 33 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N SER E 48 " --> pdb=" O MET E 67 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N MET E 67 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LYS E 63 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 31 through 35 removed outlier: 8.627A pdb=" N ILE E 31 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER E 48 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN E 33 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR E 99 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA E 49 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LYS E 97 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N PHE E 51 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 10.364A pdb=" N GLY E 95 " --> pdb=" O PHE E 51 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 83 through 86 removed outlier: 4.287A pdb=" N ASP E 109 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AB9, first strand: chain 'E' and resid 237 through 238 Processing sheet with id=AC1, first strand: chain 'E' and resid 206 through 211 Processing sheet with id=AC2, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AC3, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AC4, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AC5, first strand: chain 'F' and resid 88 through 90 removed outlier: 8.586A pdb=" N ALA F 94 " --> pdb=" O PRO F 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 116 through 119 removed outlier: 3.820A pdb=" N ALA F 127 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC8, first strand: chain 'G' and resid 2 through 8 removed outlier: 3.939A pdb=" N LYS G 160 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 15 through 19 removed outlier: 7.615A pdb=" N GLU G 30 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR G 137 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR G 32 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE G 135 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL G 34 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU G 133 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER G 36 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL G 131 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU G 38 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU G 129 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA G 127 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR G 42 " --> pdb=" O HIS G 125 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS G 125 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS G 44 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS G 123 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 140 through 147 removed outlier: 3.609A pdb=" N TYR G 46 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS G 123 " --> pdb=" O LYS G 44 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LYS G 44 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS G 125 " --> pdb=" O THR G 42 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR G 42 " --> pdb=" O HIS G 125 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA G 127 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU G 129 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU G 38 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL G 131 " --> pdb=" O SER G 36 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER G 36 " --> pdb=" O VAL G 131 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU G 133 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL G 34 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ILE G 135 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR G 32 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR G 137 " --> pdb=" O GLU G 30 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N GLU G 30 " --> pdb=" O TYR G 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 59 through 61 removed outlier: 5.955A pdb=" N ASN G 100 " --> pdb=" O GLY G 83 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AD4, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AD5, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AD6, first strand: chain 'G' and resid 301 through 303 removed outlier: 3.873A pdb=" N THR G 317 " --> pdb=" O THR G 302 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 326 through 327 removed outlier: 3.627A pdb=" N GLY G 326 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 337 through 339 Processing sheet with id=AD9, first strand: chain 'G' and resid 365 through 369 Processing sheet with id=AE1, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AE2, first strand: chain 'H' and resid 14 through 16 Processing sheet with id=AE3, first strand: chain 'H' and resid 31 through 35 removed outlier: 6.761A pdb=" N GLN H 46 " --> pdb=" O GLU H 32 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL H 34 " --> pdb=" O ARG H 44 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG H 44 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR H 99 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA H 49 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LYS H 97 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 63 through 67 Processing sheet with id=AE5, first strand: chain 'H' and resid 83 through 86 removed outlier: 4.262A pdb=" N ASP H 109 " --> pdb=" O LYS H 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 150 through 155 Processing sheet with id=AE7, first strand: chain 'H' and resid 237 through 238 Processing sheet with id=AE8, first strand: chain 'H' and resid 180 through 183 Processing sheet with id=AE9, first strand: chain 'H' and resid 206 through 211 removed outlier: 3.623A pdb=" N GLU H 200 " --> pdb=" O ILE H 227 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 275 through 279 Processing sheet with id=AF2, first strand: chain 'I' and resid 34 through 36 removed outlier: 4.252A pdb=" N LYS I 44 " --> pdb=" O MET I 19 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 96 through 98 removed outlier: 5.053A pdb=" N PHE I 102 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL I 144 " --> pdb=" O VAL I 129 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL I 129 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 117 through 119 removed outlier: 3.738A pdb=" N ALA I 127 " --> pdb=" O ILE I 118 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL I 129 " --> pdb=" O VAL I 144 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL I 144 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 2 through 8 removed outlier: 3.817A pdb=" N LYS J 160 " --> pdb=" O ASP J 281 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 12 through 19 removed outlier: 5.827A pdb=" N ILE J 13 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL J 33 " --> pdb=" O ILE J 13 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR J 32 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE J 135 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL J 34 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU J 133 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER J 36 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL J 131 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU J 38 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU J 129 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA J 127 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR J 42 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS J 125 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 142 through 148 removed outlier: 4.667A pdb=" N LEU J 129 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR J 46 " --> pdb=" O ALA J 121 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LYS J 123 " --> pdb=" O LYS J 44 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS J 44 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N HIS J 125 " --> pdb=" O THR J 42 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR J 42 " --> pdb=" O HIS J 125 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA J 127 " --> pdb=" O PRO J 40 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU J 129 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU J 38 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL J 131 " --> pdb=" O SER J 36 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER J 36 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU J 133 " --> pdb=" O VAL J 34 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL J 34 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE J 135 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR J 32 " --> pdb=" O ILE J 135 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 59 through 61 removed outlier: 5.949A pdb=" N ASN J 100 " --> pdb=" O GLY J 83 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 87 through 88 removed outlier: 3.770A pdb=" N MET J 88 " --> pdb=" O GLY J 91 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AG2, first strand: chain 'J' and resid 219 through 221 Processing sheet with id=AG3, first strand: chain 'J' and resid 296 through 304 removed outlier: 4.565A pdb=" N GLU J 298 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER J 315 " --> pdb=" O ALA J 304 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 306 through 307 removed outlier: 7.067A pdb=" N CYS J 306 " --> pdb=" O LYS J 381 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 387 through 388 removed outlier: 3.619A pdb=" N THR K 275 " --> pdb=" O HIS K 286 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 387 through 388 removed outlier: 7.299A pdb=" N LEU K 285 " --> pdb=" O PHE K 319 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE K 319 " --> pdb=" O LEU K 285 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU K 287 " --> pdb=" O ARG K 317 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ARG K 317 " --> pdb=" O LEU K 287 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ALA K 289 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR K 315 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG K 291 " --> pdb=" O GLY K 313 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY K 313 " --> pdb=" O ARG K 291 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 14 through 16 Processing sheet with id=AG8, first strand: chain 'K' and resid 18 through 19 removed outlier: 4.140A pdb=" N TYR K 18 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP K 109 " --> pdb=" O LYS K 128 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 31 through 35 removed outlier: 3.928A pdb=" N ASN K 33 " --> pdb=" O GLN K 46 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN K 104 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG K 93 " --> pdb=" O GLN K 104 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 63 through 67 Processing sheet with id=AH2, first strand: chain 'K' and resid 150 through 155 Processing sheet with id=AH3, first strand: chain 'K' and resid 237 through 238 removed outlier: 3.677A pdb=" N GLY K 164 " --> pdb=" O ILE K 257 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY K 253 " --> pdb=" O MET K 168 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 207 through 211 removed outlier: 3.608A pdb=" N VAL K 211 " --> pdb=" O VAL K 197 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 15 through 16 Processing sheet with id=AH6, first strand: chain 'L' and resid 18 through 19 Processing sheet with id=AH7, first strand: chain 'L' and resid 56 through 58 Processing sheet with id=AH8, first strand: chain 'L' and resid 88 through 90 removed outlier: 8.722A pdb=" N ALA L 94 " --> pdb=" O PRO L 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL L 104 " --> pdb=" O THR L 139 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG L 138 " --> pdb=" O GLU L 135 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.685A pdb=" N ALA L 127 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE L 128 " --> pdb=" O VAL L 144 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL L 144 " --> pdb=" O ILE L 128 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'M' and resid 2 through 6 removed outlier: 6.270A pdb=" N LEU M 2 " --> pdb=" O GLU M 91 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU M 93 " --> pdb=" O LEU M 2 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR M 4 " --> pdb=" O GLU M 93 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 15 through 18 removed outlier: 7.103A pdb=" N PHE M 15 " --> pdb=" O VAL M 57 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL M 57 " --> pdb=" O PHE M 15 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL M 54 " --> pdb=" O ASN M 49 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 2 through 6 removed outlier: 5.949A pdb=" N LEU N 2 " --> pdb=" O GLU N 91 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU N 93 " --> pdb=" O LEU N 2 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR N 4 " --> pdb=" O GLU N 93 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 15 through 18 removed outlier: 7.289A pdb=" N PHE N 15 " --> pdb=" O VAL N 57 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL N 57 " --> pdb=" O PHE N 15 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL N 54 " --> pdb=" O ASN N 49 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'O' and resid 2 through 6 removed outlier: 6.302A pdb=" N LEU O 2 " --> pdb=" O GLU O 91 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLU O 93 " --> pdb=" O LEU O 2 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR O 4 " --> pdb=" O GLU O 93 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'O' and resid 15 through 18 removed outlier: 6.999A pdb=" N PHE O 15 " --> pdb=" O VAL O 57 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL O 57 " --> pdb=" O PHE O 15 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.720A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'A' and resid 12 through 19 removed outlier: 4.182A pdb=" N VAL A 33 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE A 31 " --> pdb=" O PRO A 14 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 16 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 29 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 18 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU A 27 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 39 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 128 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.814A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 128 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 39 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL A 136 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE A 31 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 59 through 62 Processing sheet with id=AJ2, first strand: chain 'A' and resid 203 through 205 Processing sheet with id=AJ3, first strand: chain 'A' and resid 219 through 221 Processing sheet with id=AJ4, first strand: chain 'A' and resid 296 through 304 removed outlier: 3.776A pdb=" N GLU A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'A' and resid 328 through 329 Processing sheet with id=AJ6, first strand: chain 'A' and resid 365 through 369 removed outlier: 3.885A pdb=" N LEU A 369 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AJ8, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.433A pdb=" N HIS B 256 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY B 164 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AK1, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.177A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TYR B 99 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA B 49 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS B 97 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'B' and resid 63 through 67 Processing sheet with id=AK3, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.391A pdb=" N ASP B 109 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'B' and resid 150 through 155 Processing sheet with id=AK5, first strand: chain 'B' and resid 180 through 183 Processing sheet with id=AK6, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AK7, first strand: chain 'B' and resid 275 through 278 Processing sheet with id=AK8, first strand: chain 'C' and resid 24 through 29 removed outlier: 4.247A pdb=" N GLY C 26 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'C' and resid 36 through 38 Processing sheet with id=AL1, first strand: chain 'C' and resid 88 through 90 removed outlier: 3.714A pdb=" N GLN C 96 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'C' and resid 117 through 119 removed outlier: 8.655A pdb=" N VAL C 126 " --> pdb=" O TRP C 146 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP C 146 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER C 142 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 143 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 2 through 7 removed outlier: 3.620A pdb=" N GLN P 36 " --> pdb=" O PHE P 80 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'P' and resid 15 through 18 removed outlier: 7.451A pdb=" N PHE P 15 " --> pdb=" O VAL P 57 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL P 57 " --> pdb=" O PHE P 15 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY P 17 " --> pdb=" O LEU P 55 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL P 54 " --> pdb=" O ASN P 49 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 2859 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: 14.62 Time building geometry restraints manager: 8.83 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: 10907 1.34 - 1.47: 8508 1.47 - 1.60: 14863 1.60 - 1.73: 0 1.73 - 1.86: 254 Bond restraints: 34532 Sorted by residual: bond pdb=" CA ASP H 36 " pdb=" CB ASP H 36 " ideal model delta sigma weight residual 1.531 1.599 -0.068 3.12e-02 1.03e+03 4.77e+00 bond pdb=" C THR B 398 " pdb=" N PRO B 399 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.62e+00 bond pdb=" C CYS B 16 " pdb=" N PRO B 17 " ideal model delta sigma weight residual 1.337 1.364 -0.027 1.24e-02 6.50e+03 4.61e+00 bond pdb=" N ASN L 99 " pdb=" CA ASN L 99 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.94e+00 bond pdb=" CB ASN G 139 " pdb=" CG ASN G 139 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.22e+00 ... (remaining 34527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 45701 2.42 - 4.85: 1089 4.85 - 7.27: 158 7.27 - 9.69: 31 9.69 - 12.11: 10 Bond angle restraints: 46989 Sorted by residual: angle pdb=" C CYS D 94 " pdb=" N PHE D 95 " pdb=" CA PHE D 95 " ideal model delta sigma weight residual 120.95 132.74 -11.79 1.78e+00 3.16e-01 4.39e+01 angle pdb=" C GLY G 138 " pdb=" N ASN G 139 " pdb=" CA ASN G 139 " ideal model delta sigma weight residual 126.32 137.62 -11.30 1.74e+00 3.30e-01 4.22e+01 angle pdb=" N VAL B 135 " pdb=" CA VAL B 135 " pdb=" C VAL B 135 " ideal model delta sigma weight residual 113.71 108.10 5.61 9.50e-01 1.11e+00 3.48e+01 angle pdb=" N VAL I 104 " pdb=" CA VAL I 104 " pdb=" C VAL I 104 " ideal model delta sigma weight residual 108.45 102.13 6.32 1.20e+00 6.94e-01 2.77e+01 angle pdb=" N GLY I 86 " pdb=" CA GLY I 86 " pdb=" C GLY I 86 " ideal model delta sigma weight residual 111.78 120.19 -8.41 1.69e+00 3.50e-01 2.47e+01 ... (remaining 46984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 19152 17.87 - 35.75: 1417 35.75 - 53.62: 267 53.62 - 71.50: 69 71.50 - 89.37: 18 Dihedral angle restraints: 20923 sinusoidal: 8440 harmonic: 12483 Sorted by residual: dihedral pdb=" CB CYS H 152 " pdb=" SG CYS H 152 " pdb=" SG CYS H 266 " pdb=" CB CYS H 266 " ideal model delta sinusoidal sigma weight residual -86.00 -175.37 89.37 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS E 152 " pdb=" SG CYS E 152 " pdb=" SG CYS E 266 " pdb=" CB CYS E 266 " ideal model delta sinusoidal sigma weight residual 93.00 177.11 -84.11 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS K 16 " pdb=" SG CYS K 16 " pdb=" SG CYS K 124 " pdb=" CB CYS K 124 " ideal model delta sinusoidal sigma weight residual 93.00 171.76 -78.76 1 1.00e+01 1.00e-02 7.73e+01 ... (remaining 20920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4860 0.098 - 0.196: 448 0.196 - 0.294: 21 0.294 - 0.391: 6 0.391 - 0.489: 2 Chirality restraints: 5337 Sorted by residual: chirality pdb=" CB ILE J 307 " pdb=" CA ILE J 307 " pdb=" CG1 ILE J 307 " pdb=" CG2 ILE J 307 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB ILE G 307 " pdb=" CA ILE G 307 " pdb=" CG1 ILE G 307 " pdb=" CG2 ILE G 307 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB ILE D 307 " pdb=" CA ILE D 307 " pdb=" CG1 ILE D 307 " pdb=" CG2 ILE D 307 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 5334 not shown) Planarity restraints: 6033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 409 " -0.019 2.00e-02 2.50e+03 2.20e-02 1.22e+01 pdb=" CG TRP G 409 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP G 409 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP G 409 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 409 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 409 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP G 409 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 409 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 409 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G 409 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 137 " -0.263 9.50e-02 1.11e+02 1.18e-01 8.64e+00 pdb=" NE ARG H 137 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 137 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG H 137 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG H 137 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 137 " 0.258 9.50e-02 1.11e+02 1.16e-01 8.25e+00 pdb=" NE ARG E 137 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG E 137 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG E 137 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG E 137 " 0.009 2.00e-02 2.50e+03 ... (remaining 6030 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3235 2.75 - 3.29: 32052 3.29 - 3.83: 55927 3.83 - 4.36: 64663 4.36 - 4.90: 112271 Nonbonded interactions: 268148 Sorted by model distance: nonbonded pdb=" OD2 ASP A 75 " pdb=" OG1 THR A 217 " model vdw 2.215 3.040 nonbonded pdb=" OG SER K 79 " pdb=" OE1 GLU K 81 " model vdw 2.219 3.040 nonbonded pdb=" OG SER J 360 " pdb=" O GLN J 362 " model vdw 2.228 3.040 nonbonded pdb=" O PRO I 84 " pdb=" OH TYR I 88 " model vdw 2.231 3.040 nonbonded pdb=" OG SER D 360 " pdb=" O GLN D 362 " model vdw 2.236 3.040 ... (remaining 268143 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' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = (chain 'B' and (resid 1 through 117 or resid 121 through 403 or resid 501 throug \ h 502)) selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 6 through 71 or resid 75 through 163)) selection = (chain 'I' and (resid 6 through 71 or resid 75 through 163)) selection = (chain 'L' and (resid 6 through 71 or resid 75 through 163)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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 individual isotropic 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: 1.630 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: 0.040 Extract box with map and model: 1.480 Check model and map are aligned: 0.260 Set scattering table: 0.350 Process input model: 74.340 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.200 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 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 : 0.004 0.068 34608 Z= 0.180 Angle : 0.904 12.114 47157 Z= 0.470 Chirality : 0.056 0.489 5337 Planarity : 0.007 0.118 6017 Dihedral : 12.766 88.193 12741 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.12), residues: 4280 helix: -0.17 (0.22), residues: 439 sheet: -0.47 (0.14), residues: 1302 loop : -1.41 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP G 409 HIS 0.017 0.001 HIS K 174 PHE 0.037 0.002 PHE J 170 TYR 0.026 0.002 TYR D 46 ARG 0.022 0.001 ARG L 138 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 16) link_NAG-ASN : angle 2.84076 ( 48) hydrogen bonds : bond 0.12771 ( 1082) hydrogen bonds : angle 6.83923 ( 2859) SS BOND : bond 0.00483 ( 60) SS BOND : angle 2.42673 ( 120) covalent geometry : bond 0.00373 (34532) covalent geometry : angle 0.89242 (46989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1161 time to evaluate : 3.978 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: D 18 LEU cc_start: 0.7596 (tt) cc_final: 0.7367 (tp) REVERT: D 27 LEU cc_start: 0.8055 (tp) cc_final: 0.7813 (tp) REVERT: D 43 ASN cc_start: 0.8577 (p0) cc_final: 0.8366 (p0) REVERT: D 97 ASP cc_start: 0.7490 (p0) cc_final: 0.7220 (p0) REVERT: D 113 ASP cc_start: 0.7791 (m-30) cc_final: 0.7559 (m-30) REVERT: D 143 ARG cc_start: 0.7409 (mpp-170) cc_final: 0.7202 (mpp-170) REVERT: D 264 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7526 (mm-30) REVERT: D 267 ARG cc_start: 0.8160 (ptt-90) cc_final: 0.7740 (ptt-90) REVERT: D 299 VAL cc_start: 0.8206 (t) cc_final: 0.7553 (t) REVERT: D 336 THR cc_start: 0.7853 (m) cc_final: 0.7641 (p) REVERT: D 408 ASN cc_start: 0.7923 (m-40) cc_final: 0.7704 (m-40) REVERT: E 126 VAL cc_start: 0.8645 (t) cc_final: 0.8439 (m) REVERT: E 140 TYR cc_start: 0.8794 (p90) cc_final: 0.8478 (p90) REVERT: E 200 GLU cc_start: 0.7152 (tt0) cc_final: 0.6795 (tt0) REVERT: E 303 ARG cc_start: 0.7411 (ttt90) cc_final: 0.7005 (ttt90) REVERT: E 388 CYS cc_start: 0.7795 (p) cc_final: 0.7447 (m) REVERT: F 8 MET cc_start: 0.6640 (mmm) cc_final: 0.6251 (mmm) REVERT: F 60 MET cc_start: 0.7517 (mmp) cc_final: 0.7291 (mmp) REVERT: G 130 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7717 (mmmm) REVERT: G 191 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7404 (mm-30) REVERT: G 264 GLU cc_start: 0.7701 (mp0) cc_final: 0.7297 (mp0) REVERT: G 278 ILE cc_start: 0.8377 (mm) cc_final: 0.8136 (mm) REVERT: G 323 ASN cc_start: 0.7949 (p0) cc_final: 0.7624 (p0) REVERT: G 324 ARG cc_start: 0.7418 (mtm-85) cc_final: 0.7099 (mtp-110) REVERT: G 365 PHE cc_start: 0.7724 (p90) cc_final: 0.7499 (p90) REVERT: G 428 LEU cc_start: 0.8012 (mt) cc_final: 0.7482 (mt) REVERT: G 432 SER cc_start: 0.8323 (t) cc_final: 0.8118 (p) REVERT: H 37 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7408 (mm-30) REVERT: H 78 ASP cc_start: 0.7705 (t0) cc_final: 0.7371 (t0) REVERT: H 99 TYR cc_start: 0.8483 (m-10) cc_final: 0.8204 (m-80) REVERT: H 151 LYS cc_start: 0.8637 (tttm) cc_final: 0.8357 (tttm) REVERT: H 179 TYR cc_start: 0.7958 (m-10) cc_final: 0.7662 (m-10) REVERT: H 181 GLU cc_start: 0.6641 (mp0) cc_final: 0.6320 (mp0) REVERT: H 211 VAL cc_start: 0.7872 (m) cc_final: 0.7549 (p) REVERT: H 239 ASN cc_start: 0.7815 (p0) cc_final: 0.7303 (t0) REVERT: H 278 LYS cc_start: 0.8510 (mtmm) cc_final: 0.8202 (mttp) REVERT: I 8 MET cc_start: 0.5170 (mmt) cc_final: 0.4899 (mmt) REVERT: I 19 MET cc_start: 0.6962 (tpt) cc_final: 0.6639 (tpt) REVERT: I 20 LEU cc_start: 0.6607 (mp) cc_final: 0.6299 (mp) REVERT: I 37 LYS cc_start: 0.7869 (tmmt) cc_final: 0.7479 (tmmt) REVERT: I 55 LEU cc_start: 0.8313 (mp) cc_final: 0.8104 (mp) REVERT: J 7 VAL cc_start: 0.8625 (p) cc_final: 0.8341 (m) REVERT: J 123 LYS cc_start: 0.8114 (mttt) cc_final: 0.7586 (mttp) REVERT: J 175 HIS cc_start: 0.7360 (t70) cc_final: 0.7080 (t70) REVERT: J 212 ASP cc_start: 0.7846 (t0) cc_final: 0.7602 (t0) REVERT: J 234 THR cc_start: 0.8545 (t) cc_final: 0.8290 (m) REVERT: J 289 ARG cc_start: 0.7615 (mmp-170) cc_final: 0.7406 (mmp-170) REVERT: J 338 VAL cc_start: 0.8126 (t) cc_final: 0.7898 (p) REVERT: J 340 LYS cc_start: 0.8453 (tttt) cc_final: 0.8195 (tttt) REVERT: J 372 LYS cc_start: 0.7939 (tptm) cc_final: 0.7639 (tptm) REVERT: J 408 ASN cc_start: 0.7683 (m-40) cc_final: 0.7134 (m-40) REVERT: K 60 ASP cc_start: 0.7519 (t0) cc_final: 0.7263 (t0) REVERT: K 109 ASP cc_start: 0.7778 (m-30) cc_final: 0.7533 (m-30) REVERT: K 151 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7975 (ttmm) REVERT: K 170 ARG cc_start: 0.8347 (ptp-110) cc_final: 0.8039 (ptp90) REVERT: K 206 TYR cc_start: 0.8090 (t80) cc_final: 0.7844 (t80) REVERT: K 224 LYS cc_start: 0.8286 (ptmt) cc_final: 0.8030 (ptmt) REVERT: K 290 THR cc_start: 0.8390 (m) cc_final: 0.8149 (p) REVERT: K 334 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7616 (mm-30) REVERT: K 371 LEU cc_start: 0.8194 (mp) cc_final: 0.7988 (mm) REVERT: L 146 TRP cc_start: 0.7070 (m-90) cc_final: 0.6826 (m-90) REVERT: L 149 LYS cc_start: 0.8087 (ptpt) cc_final: 0.7843 (ptpt) REVERT: A 15 TYR cc_start: 0.7830 (t80) cc_final: 0.7530 (t80) REVERT: A 32 THR cc_start: 0.7894 (p) cc_final: 0.7669 (p) REVERT: A 37 GLU cc_start: 0.7759 (pt0) cc_final: 0.7378 (pt0) REVERT: A 45 GLU cc_start: 0.7545 (tp30) cc_final: 0.7225 (tp30) REVERT: A 188 ASP cc_start: 0.8277 (t0) cc_final: 0.7961 (t0) REVERT: A 202 ASP cc_start: 0.7819 (p0) cc_final: 0.7603 (p0) REVERT: A 206 SER cc_start: 0.8513 (p) cc_final: 0.8288 (p) REVERT: A 216 ARG cc_start: 0.7746 (ttt180) cc_final: 0.7479 (ttt180) REVERT: A 218 ASP cc_start: 0.7907 (t0) cc_final: 0.7430 (t0) REVERT: A 237 VAL cc_start: 0.8850 (p) cc_final: 0.8555 (m) REVERT: A 240 TYR cc_start: 0.8445 (t80) cc_final: 0.8140 (t80) REVERT: A 242 MET cc_start: 0.7861 (mmm) cc_final: 0.7576 (tpp) REVERT: A 381 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7984 (mtmm) REVERT: A 395 ASP cc_start: 0.7304 (t70) cc_final: 0.7083 (t70) REVERT: A 433 MET cc_start: 0.7261 (mmm) cc_final: 0.7040 (mmm) REVERT: B 6 PHE cc_start: 0.8312 (m-80) cc_final: 0.7949 (m-80) REVERT: B 19 CYS cc_start: 0.6766 (m) cc_final: 0.6483 (m) REVERT: B 25 CYS cc_start: 0.6064 (p) cc_final: 0.5653 (p) REVERT: B 158 LEU cc_start: 0.8338 (tp) cc_final: 0.8098 (tt) REVERT: B 177 LYS cc_start: 0.8045 (ttpp) cc_final: 0.7700 (ttpp) REVERT: B 178 SER cc_start: 0.8271 (m) cc_final: 0.7960 (t) REVERT: B 199 TYR cc_start: 0.6310 (p90) cc_final: 0.5805 (p90) REVERT: B 230 LYS cc_start: 0.8286 (mttm) cc_final: 0.8056 (mttm) REVERT: B 324 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 394 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7550 (mmp80) REVERT: C 37 LYS cc_start: 0.8283 (tmtt) cc_final: 0.7807 (tmtt) REVERT: C 60 MET cc_start: 0.6765 (mmp) cc_final: 0.6421 (mmp) REVERT: C 61 TYR cc_start: 0.7894 (m-10) cc_final: 0.7576 (m-80) outliers start: 0 outliers final: 0 residues processed: 1161 average time/residue: 0.4730 time to fit residues: 854.0521 Evaluate side-chains 1060 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1060 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 361 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 110 optimal weight: 0.1980 chunk 218 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 388 optimal weight: 10.0000 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 HIS ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN G 408 ASN H 46 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 HIS J 228 ASN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN ** L 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** A 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.138803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118532 restraints weight = 56631.494| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.68 r_work: 0.3283 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 34608 Z= 0.383 Angle : 0.794 11.139 47157 Z= 0.407 Chirality : 0.053 0.306 5337 Planarity : 0.006 0.072 6017 Dihedral : 6.597 56.476 4997 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 2.47 % Allowed : 9.98 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4280 helix: 0.55 (0.23), residues: 475 sheet: -0.53 (0.14), residues: 1297 loop : -1.34 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 90 HIS 0.007 0.002 HIS J 331 PHE 0.044 0.003 PHE H 134 TYR 0.032 0.003 TYR D 46 ARG 0.010 0.001 ARG K 291 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 16) link_NAG-ASN : angle 2.71561 ( 48) hydrogen bonds : bond 0.04401 ( 1082) hydrogen bonds : angle 5.86635 ( 2859) SS BOND : bond 0.00512 ( 60) SS BOND : angle 2.26394 ( 120) covalent geometry : bond 0.00845 (34532) covalent geometry : angle 0.78184 (46989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1137 time to evaluate : 3.746 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: D 18 LEU cc_start: 0.7773 (tt) cc_final: 0.7526 (tp) REVERT: D 45 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7089 (tm-30) REVERT: D 46 TYR cc_start: 0.7785 (p90) cc_final: 0.7236 (p90) REVERT: D 321 LYS cc_start: 0.8057 (mmtm) cc_final: 0.7570 (mmtm) REVERT: D 324 ARG cc_start: 0.8537 (ttp-110) cc_final: 0.8236 (ttp-110) REVERT: D 336 THR cc_start: 0.7895 (m) cc_final: 0.7643 (p) REVERT: D 406 SER cc_start: 0.8638 (t) cc_final: 0.8239 (p) REVERT: D 408 ASN cc_start: 0.8100 (m-40) cc_final: 0.7863 (m-40) REVERT: E 18 TYR cc_start: 0.8116 (t80) cc_final: 0.7824 (t80) REVERT: E 74 ASP cc_start: 0.7563 (p0) cc_final: 0.7299 (p0) REVERT: E 131 ARG cc_start: 0.8222 (mmt-90) cc_final: 0.7977 (mmt-90) REVERT: E 200 GLU cc_start: 0.7196 (tt0) cc_final: 0.6771 (tt0) REVERT: E 252 GLN cc_start: 0.8383 (mm110) cc_final: 0.8120 (mp10) REVERT: E 255 LEU cc_start: 0.8906 (mp) cc_final: 0.8677 (mt) REVERT: E 303 ARG cc_start: 0.7666 (ttt90) cc_final: 0.7262 (ttt90) REVERT: E 354 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7325 (mt-10) REVERT: E 355 ILE cc_start: 0.8428 (mp) cc_final: 0.8136 (mp) REVERT: E 388 CYS cc_start: 0.7824 (p) cc_final: 0.7522 (m) REVERT: F 8 MET cc_start: 0.6840 (mmm) cc_final: 0.6490 (mmm) REVERT: F 60 MET cc_start: 0.7847 (mmp) cc_final: 0.7609 (mmp) REVERT: G 9 ASN cc_start: 0.7827 (t0) cc_final: 0.7532 (t0) REVERT: G 99 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7149 (tm-30) REVERT: G 130 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8075 (ttmm) REVERT: G 264 GLU cc_start: 0.7767 (mp0) cc_final: 0.7377 (mp0) REVERT: G 338 VAL cc_start: 0.8743 (p) cc_final: 0.8508 (t) REVERT: G 341 GLU cc_start: 0.8198 (mp0) cc_final: 0.7511 (mp0) REVERT: G 428 LEU cc_start: 0.8206 (mt) cc_final: 0.7821 (mt) REVERT: H 36 ASP cc_start: 0.7669 (p0) cc_final: 0.7317 (p0) REVERT: H 37 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7563 (mm-30) REVERT: H 60 ASP cc_start: 0.7886 (t0) cc_final: 0.7650 (t0) REVERT: H 76 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8290 (mtmm) REVERT: H 78 ASP cc_start: 0.7857 (t0) cc_final: 0.7492 (t0) REVERT: H 82 LYS cc_start: 0.8266 (ptpt) cc_final: 0.7702 (ptpt) REVERT: H 105 CYS cc_start: 0.7579 (m) cc_final: 0.7278 (m) REVERT: H 133 LYS cc_start: 0.8518 (mtpp) cc_final: 0.8246 (mttm) REVERT: H 134 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.6245 (m-10) REVERT: H 151 LYS cc_start: 0.8603 (tttm) cc_final: 0.8342 (tttm) REVERT: H 181 GLU cc_start: 0.6708 (mp0) cc_final: 0.6478 (mp0) REVERT: H 211 VAL cc_start: 0.7817 (m) cc_final: 0.7490 (p) REVERT: H 260 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7951 (ttp-170) REVERT: H 278 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8206 (mttm) REVERT: I 8 MET cc_start: 0.4983 (mmt) cc_final: 0.4706 (mmt) REVERT: I 19 MET cc_start: 0.6841 (tpt) cc_final: 0.6573 (tpt) REVERT: I 37 LYS cc_start: 0.8107 (tmmt) cc_final: 0.7633 (tmmt) REVERT: I 88 TYR cc_start: 0.6705 (m-80) cc_final: 0.6474 (m-80) REVERT: J 7 VAL cc_start: 0.8532 (p) cc_final: 0.8266 (m) REVERT: J 105 GLU cc_start: 0.7492 (tt0) cc_final: 0.7260 (mt-10) REVERT: J 212 ASP cc_start: 0.7987 (t0) cc_final: 0.7670 (t0) REVERT: J 220 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7705 (mtt90) REVERT: J 234 THR cc_start: 0.8612 (t) cc_final: 0.8329 (m) REVERT: J 289 ARG cc_start: 0.7764 (mmp-170) cc_final: 0.7469 (mmp-170) REVERT: J 372 LYS cc_start: 0.8107 (tptm) cc_final: 0.7767 (tptm) REVERT: J 388 ILE cc_start: 0.8787 (tp) cc_final: 0.8508 (tt) REVERT: J 408 ASN cc_start: 0.7839 (m-40) cc_final: 0.7342 (m-40) REVERT: K 3 THR cc_start: 0.8148 (t) cc_final: 0.7863 (p) REVERT: K 40 ASP cc_start: 0.8053 (p0) cc_final: 0.7838 (p0) REVERT: K 74 ASP cc_start: 0.7477 (p0) cc_final: 0.7168 (p0) REVERT: K 81 GLU cc_start: 0.7537 (mp0) cc_final: 0.7256 (mp0) REVERT: K 151 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8148 (ttmm) REVERT: K 224 LYS cc_start: 0.8413 (ptmt) cc_final: 0.7959 (ptmt) REVERT: K 266 CYS cc_start: 0.7504 (p) cc_final: 0.7027 (p) REVERT: K 334 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7775 (mm-30) REVERT: L 37 LYS cc_start: 0.7737 (tmtt) cc_final: 0.7330 (tmtt) REVERT: L 62 ASP cc_start: 0.7840 (t0) cc_final: 0.7107 (t0) REVERT: L 149 LYS cc_start: 0.8270 (ptpt) cc_final: 0.7987 (ptpt) REVERT: A 32 THR cc_start: 0.7967 (p) cc_final: 0.7742 (p) REVERT: A 45 GLU cc_start: 0.7659 (tp30) cc_final: 0.7340 (tp30) REVERT: A 105 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 134 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7376 (ttp-110) REVERT: A 188 ASP cc_start: 0.8211 (t0) cc_final: 0.7936 (t0) REVERT: A 202 ASP cc_start: 0.7907 (p0) cc_final: 0.7683 (p0) REVERT: A 262 GLU cc_start: 0.7648 (mp0) cc_final: 0.6898 (mp0) REVERT: A 264 GLU cc_start: 0.7416 (pm20) cc_final: 0.7174 (pm20) REVERT: A 365 PHE cc_start: 0.7986 (p90) cc_final: 0.7182 (p90) REVERT: A 379 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 381 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8106 (mtmm) REVERT: A 433 MET cc_start: 0.7379 (mmm) cc_final: 0.7027 (mmm) REVERT: B 6 PHE cc_start: 0.8348 (m-80) cc_final: 0.7497 (m-80) REVERT: B 19 CYS cc_start: 0.6849 (m) cc_final: 0.6544 (m) REVERT: B 105 CYS cc_start: 0.7989 (m) cc_final: 0.7539 (m) REVERT: B 132 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8082 (mtm-85) REVERT: B 158 LEU cc_start: 0.8617 (tp) cc_final: 0.8391 (tt) REVERT: B 177 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7896 (ttpp) REVERT: B 216 LYS cc_start: 0.8217 (tttm) cc_final: 0.7800 (tttm) REVERT: B 230 LYS cc_start: 0.8353 (mttm) cc_final: 0.8101 (mttm) REVERT: B 266 CYS cc_start: 0.6870 (m) cc_final: 0.6497 (m) REVERT: B 305 ASP cc_start: 0.7510 (m-30) cc_final: 0.7214 (m-30) REVERT: B 324 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 394 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7714 (mmp80) REVERT: B 400 TYR cc_start: 0.7530 (t80) cc_final: 0.7082 (t80) REVERT: C 37 LYS cc_start: 0.8452 (tmtt) cc_final: 0.7816 (tmtt) REVERT: C 97 TYR cc_start: 0.6619 (t80) cc_final: 0.6415 (t80) outliers start: 91 outliers final: 72 residues processed: 1164 average time/residue: 0.5005 time to fit residues: 906.2541 Evaluate side-chains 1168 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1095 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 21 HIS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 134 PHE Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 291 SER Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 144 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 270 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 250 optimal weight: 0.7980 chunk 290 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 273 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 340 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 319 GLN ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN G 204 GLN G 408 ASN H 50 GLN I 92 HIS J 43 ASN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS M 10 GLN A 319 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS C 89 ASN ** C 92 HIS ** 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 = 0.3792 r_free = 0.3792 target = 0.155906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135746 restraints weight = 55904.991| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.72 r_work: 0.3337 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34608 Z= 0.124 Angle : 0.645 13.291 47157 Z= 0.323 Chirality : 0.047 0.286 5337 Planarity : 0.005 0.062 6017 Dihedral : 5.958 56.450 4997 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.51 % Favored : 94.44 % Rotamer: Outliers : 2.30 % Allowed : 14.45 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4280 helix: 1.07 (0.23), residues: 475 sheet: -0.41 (0.14), residues: 1306 loop : -1.17 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 90 HIS 0.006 0.001 HIS B 363 PHE 0.024 0.001 PHE H 134 TYR 0.028 0.001 TYR D 320 ARG 0.008 0.001 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 16) link_NAG-ASN : angle 2.30417 ( 48) hydrogen bonds : bond 0.03439 ( 1082) hydrogen bonds : angle 5.45242 ( 2859) SS BOND : bond 0.00272 ( 60) SS BOND : angle 1.53026 ( 120) covalent geometry : bond 0.00283 (34532) covalent geometry : angle 0.63736 (46989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1109 time to evaluate : 3.715 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: D 18 LEU cc_start: 0.7743 (tt) cc_final: 0.7381 (tp) REVERT: D 45 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7479 (tm-30) REVERT: D 264 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 321 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7744 (mmtm) REVERT: D 324 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.8191 (ttp-110) REVERT: D 336 THR cc_start: 0.7868 (m) cc_final: 0.7663 (p) REVERT: D 345 HIS cc_start: 0.8416 (t-90) cc_final: 0.8174 (t70) REVERT: D 406 SER cc_start: 0.8626 (t) cc_final: 0.7998 (p) REVERT: E 74 ASP cc_start: 0.7596 (p0) cc_final: 0.7304 (p0) REVERT: E 168 MET cc_start: 0.7415 (mmm) cc_final: 0.7196 (mtp) REVERT: E 181 GLU cc_start: 0.7196 (mp0) cc_final: 0.6980 (mp0) REVERT: E 189 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7435 (mp) REVERT: E 200 GLU cc_start: 0.7020 (tt0) cc_final: 0.6578 (tt0) REVERT: E 242 ASP cc_start: 0.7328 (t0) cc_final: 0.7113 (t0) REVERT: E 303 ARG cc_start: 0.7654 (ttt90) cc_final: 0.7177 (ttt90) REVERT: E 334 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 354 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7273 (mt-10) REVERT: E 355 ILE cc_start: 0.8336 (mp) cc_final: 0.8080 (mp) REVERT: E 388 CYS cc_start: 0.7870 (p) cc_final: 0.7454 (m) REVERT: F 8 MET cc_start: 0.6721 (mmm) cc_final: 0.6382 (mmm) REVERT: F 60 MET cc_start: 0.7711 (mmp) cc_final: 0.7454 (mmp) REVERT: G 9 ASN cc_start: 0.7758 (t0) cc_final: 0.7435 (t0) REVERT: G 52 HIS cc_start: 0.8262 (t-90) cc_final: 0.8010 (t70) REVERT: G 99 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7101 (tm-30) REVERT: G 130 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8038 (ttmm) REVERT: G 264 GLU cc_start: 0.7745 (mp0) cc_final: 0.7341 (mp0) REVERT: G 338 VAL cc_start: 0.8715 (p) cc_final: 0.8468 (t) REVERT: G 341 GLU cc_start: 0.8124 (mp0) cc_final: 0.7528 (mp0) REVERT: G 365 PHE cc_start: 0.8039 (p90) cc_final: 0.7554 (p90) REVERT: G 367 VAL cc_start: 0.8453 (t) cc_final: 0.8190 (p) REVERT: G 428 LEU cc_start: 0.8175 (mt) cc_final: 0.7589 (mt) REVERT: G 432 SER cc_start: 0.8298 (t) cc_final: 0.8087 (p) REVERT: H 36 ASP cc_start: 0.7601 (p0) cc_final: 0.7133 (p0) REVERT: H 37 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7505 (mm-30) REVERT: H 60 ASP cc_start: 0.7746 (t0) cc_final: 0.7435 (t0) REVERT: H 76 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8302 (mtmm) REVERT: H 78 ASP cc_start: 0.7902 (t0) cc_final: 0.7438 (t0) REVERT: H 82 LYS cc_start: 0.8085 (ptpt) cc_final: 0.7494 (ptpt) REVERT: H 133 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8166 (mttt) REVERT: H 151 LYS cc_start: 0.8636 (tttm) cc_final: 0.8432 (tttm) REVERT: H 168 MET cc_start: 0.7965 (mmm) cc_final: 0.7032 (mmm) REVERT: H 179 TYR cc_start: 0.7809 (m-10) cc_final: 0.7601 (m-10) REVERT: H 181 GLU cc_start: 0.6677 (mp0) cc_final: 0.6377 (mp0) REVERT: H 211 VAL cc_start: 0.7772 (m) cc_final: 0.7416 (p) REVERT: H 244 ILE cc_start: 0.8175 (mm) cc_final: 0.7935 (mm) REVERT: H 278 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8248 (mttm) REVERT: H 305 ASP cc_start: 0.7924 (m-30) cc_final: 0.7585 (m-30) REVERT: H 370 VAL cc_start: 0.7859 (t) cc_final: 0.7652 (p) REVERT: H 394 ARG cc_start: 0.8145 (ptt-90) cc_final: 0.7880 (ptt-90) REVERT: I 8 MET cc_start: 0.4903 (mmt) cc_final: 0.4621 (mmt) REVERT: I 19 MET cc_start: 0.6820 (tpt) cc_final: 0.6597 (tpt) REVERT: J 7 VAL cc_start: 0.8636 (p) cc_final: 0.8373 (m) REVERT: J 43 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.8063 (p0) REVERT: J 50 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7807 (mtpp) REVERT: J 105 GLU cc_start: 0.7438 (tt0) cc_final: 0.7229 (mt-10) REVERT: J 113 ASP cc_start: 0.8090 (m-30) cc_final: 0.7822 (m-30) REVERT: J 134 ARG cc_start: 0.7644 (ttp-110) cc_final: 0.7210 (ttp80) REVERT: J 175 HIS cc_start: 0.7446 (t70) cc_final: 0.7206 (t70) REVERT: J 212 ASP cc_start: 0.7933 (t0) cc_final: 0.7644 (t0) REVERT: J 220 ARG cc_start: 0.8093 (mtt-85) cc_final: 0.7725 (mtt90) REVERT: J 234 THR cc_start: 0.8538 (t) cc_final: 0.8303 (m) REVERT: J 241 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7219 (mm-30) REVERT: J 289 ARG cc_start: 0.7678 (mmp-170) cc_final: 0.7434 (mmp-170) REVERT: J 372 LYS cc_start: 0.8043 (tptm) cc_final: 0.7700 (tptm) REVERT: J 388 ILE cc_start: 0.8718 (tp) cc_final: 0.8424 (tt) REVERT: J 408 ASN cc_start: 0.7739 (m-40) cc_final: 0.7282 (m-40) REVERT: K 3 THR cc_start: 0.8088 (t) cc_final: 0.7840 (p) REVERT: K 40 ASP cc_start: 0.7943 (p0) cc_final: 0.7678 (p0) REVERT: K 60 ASP cc_start: 0.7536 (t0) cc_final: 0.7050 (t0) REVERT: K 74 ASP cc_start: 0.7503 (p0) cc_final: 0.7211 (p0) REVERT: K 81 GLU cc_start: 0.7505 (mp0) cc_final: 0.7214 (mp0) REVERT: K 151 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8038 (ttmm) REVERT: K 206 TYR cc_start: 0.8086 (t80) cc_final: 0.7849 (t80) REVERT: K 224 LYS cc_start: 0.8319 (ptmt) cc_final: 0.7850 (ptmt) REVERT: K 334 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7760 (mm-30) REVERT: L 37 LYS cc_start: 0.7696 (tmtt) cc_final: 0.7268 (tmtt) REVERT: L 90 TRP cc_start: 0.7062 (p-90) cc_final: 0.6782 (p-90) REVERT: L 149 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7876 (ptpt) REVERT: A 15 TYR cc_start: 0.7935 (t80) cc_final: 0.7626 (t80) REVERT: A 37 GLU cc_start: 0.7676 (pt0) cc_final: 0.7398 (pt0) REVERT: A 45 GLU cc_start: 0.7551 (tp30) cc_final: 0.7220 (tp30) REVERT: A 46 TYR cc_start: 0.8532 (p90) cc_final: 0.8033 (p90) REVERT: A 188 ASP cc_start: 0.8191 (t0) cc_final: 0.7915 (t0) REVERT: A 202 ASP cc_start: 0.7896 (p0) cc_final: 0.7687 (p0) REVERT: A 262 GLU cc_start: 0.7584 (mp0) cc_final: 0.6819 (mp0) REVERT: A 264 GLU cc_start: 0.7422 (pm20) cc_final: 0.7060 (pm20) REVERT: A 379 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6595 (mm-30) REVERT: A 381 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8115 (mtmm) REVERT: A 433 MET cc_start: 0.7316 (mmm) cc_final: 0.6965 (mmm) REVERT: B 6 PHE cc_start: 0.8218 (m-80) cc_final: 0.7455 (m-80) REVERT: B 158 LEU cc_start: 0.8587 (tp) cc_final: 0.8369 (tt) REVERT: B 177 LYS cc_start: 0.8142 (ttpp) cc_final: 0.7736 (ttpp) REVERT: B 178 SER cc_start: 0.8283 (m) cc_final: 0.8047 (t) REVERT: B 199 TYR cc_start: 0.6453 (p90) cc_final: 0.5273 (p90) REVERT: B 216 LYS cc_start: 0.7947 (tttm) cc_final: 0.7581 (tttm) REVERT: B 230 LYS cc_start: 0.8345 (mttm) cc_final: 0.8082 (mttm) REVERT: B 305 ASP cc_start: 0.7480 (m-30) cc_final: 0.7127 (m-30) REVERT: B 324 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 394 ARG cc_start: 0.7865 (mmp80) cc_final: 0.7610 (mmp80) REVERT: B 400 TYR cc_start: 0.7395 (t80) cc_final: 0.6959 (t80) REVERT: C 37 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7948 (tmtt) REVERT: C 97 TYR cc_start: 0.6616 (t80) cc_final: 0.6396 (t80) outliers start: 85 outliers final: 62 residues processed: 1135 average time/residue: 0.5109 time to fit residues: 902.6115 Evaluate side-chains 1160 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1096 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 307 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain G residue 421 ILE Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain J residue 43 ASN Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 10 GLN Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 202 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 255 optimal weight: 8.9990 chunk 200 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 406 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 249 HIS ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN H 46 GLN H 146 HIS J 43 ASN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** 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 = 0.3696 r_free = 0.3696 target = 0.137969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.117733 restraints weight = 56444.592| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.68 r_work: 0.3273 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 34608 Z= 0.330 Angle : 0.733 11.884 47157 Z= 0.373 Chirality : 0.051 0.346 5337 Planarity : 0.006 0.063 6017 Dihedral : 6.153 56.302 4997 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 3.80 % Allowed : 15.29 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4280 helix: 1.12 (0.23), residues: 478 sheet: -0.44 (0.15), residues: 1218 loop : -1.33 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 90 HIS 0.007 0.001 HIS F 91 PHE 0.036 0.002 PHE K 134 TYR 0.028 0.002 TYR D 320 ARG 0.010 0.001 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 16) link_NAG-ASN : angle 2.62452 ( 48) hydrogen bonds : bond 0.04004 ( 1082) hydrogen bonds : angle 5.60072 ( 2859) SS BOND : bond 0.00469 ( 60) SS BOND : angle 2.10303 ( 120) covalent geometry : bond 0.00731 (34532) covalent geometry : angle 0.72179 (46989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1130 time to evaluate : 3.569 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: D 45 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7782 (tm-30) REVERT: D 273 TYR cc_start: 0.8589 (p90) cc_final: 0.7850 (p90) REVERT: D 321 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7942 (mmtm) REVERT: D 324 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8291 (ttp-110) REVERT: D 345 HIS cc_start: 0.8511 (t-90) cc_final: 0.8265 (t70) REVERT: D 406 SER cc_start: 0.8702 (t) cc_final: 0.8095 (p) REVERT: E 74 ASP cc_start: 0.7854 (p0) cc_final: 0.7635 (p0) REVERT: E 181 GLU cc_start: 0.7421 (mp0) cc_final: 0.7070 (mp0) REVERT: E 189 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7767 (mp) REVERT: E 200 GLU cc_start: 0.7426 (tt0) cc_final: 0.7015 (tt0) REVERT: E 242 ASP cc_start: 0.7572 (t0) cc_final: 0.7315 (t0) REVERT: E 303 ARG cc_start: 0.7981 (ttt90) cc_final: 0.7416 (ttt90) REVERT: E 334 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7874 (mm-30) REVERT: E 342 GLU cc_start: 0.7495 (pm20) cc_final: 0.7206 (pm20) REVERT: E 354 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 355 ILE cc_start: 0.8478 (mp) cc_final: 0.8146 (mp) REVERT: F 8 MET cc_start: 0.7069 (mmm) cc_final: 0.6665 (mmm) REVERT: F 60 MET cc_start: 0.8202 (mmp) cc_final: 0.7944 (mmp) REVERT: G 9 ASN cc_start: 0.7951 (t0) cc_final: 0.7665 (t0) REVERT: G 99 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7267 (tm-30) REVERT: G 105 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7694 (mt-10) REVERT: G 130 LYS cc_start: 0.8575 (ttmm) cc_final: 0.8233 (ttmm) REVERT: G 264 GLU cc_start: 0.7955 (mp0) cc_final: 0.7587 (mp0) REVERT: G 287 PHE cc_start: 0.7937 (m-80) cc_final: 0.7617 (m-80) REVERT: G 320 TYR cc_start: 0.8508 (p90) cc_final: 0.8249 (p90) REVERT: G 338 VAL cc_start: 0.8844 (p) cc_final: 0.8611 (t) REVERT: G 341 GLU cc_start: 0.8306 (mp0) cc_final: 0.7780 (mp0) REVERT: G 367 VAL cc_start: 0.8629 (t) cc_final: 0.8327 (p) REVERT: G 428 LEU cc_start: 0.8234 (mt) cc_final: 0.7656 (mt) REVERT: G 432 SER cc_start: 0.8390 (t) cc_final: 0.8165 (p) REVERT: H 36 ASP cc_start: 0.7830 (p0) cc_final: 0.7482 (p0) REVERT: H 37 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7831 (mm-30) REVERT: H 60 ASP cc_start: 0.8048 (t0) cc_final: 0.7641 (t0) REVERT: H 76 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: H 78 ASP cc_start: 0.8111 (t0) cc_final: 0.7691 (t0) REVERT: H 82 LYS cc_start: 0.8325 (ptpt) cc_final: 0.7740 (ptpt) REVERT: H 151 LYS cc_start: 0.8821 (tttm) cc_final: 0.8546 (tttm) REVERT: H 168 MET cc_start: 0.8324 (mmm) cc_final: 0.7513 (mmm) REVERT: H 179 TYR cc_start: 0.8087 (m-10) cc_final: 0.7859 (m-10) REVERT: H 181 GLU cc_start: 0.6819 (mp0) cc_final: 0.6438 (mp0) REVERT: H 211 VAL cc_start: 0.8000 (m) cc_final: 0.7668 (p) REVERT: H 260 ARG cc_start: 0.8435 (ttp-110) cc_final: 0.8170 (ttp-170) REVERT: H 278 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8357 (mttm) REVERT: H 305 ASP cc_start: 0.8256 (m-30) cc_final: 0.7826 (m-30) REVERT: H 394 ARG cc_start: 0.8429 (ptt-90) cc_final: 0.8170 (ptt-90) REVERT: I 8 MET cc_start: 0.5356 (mmt) cc_final: 0.5009 (mmt) REVERT: I 19 MET cc_start: 0.7326 (tpt) cc_final: 0.7047 (tpt) REVERT: J 7 VAL cc_start: 0.8706 (p) cc_final: 0.8429 (m) REVERT: J 134 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7360 (ttp80) REVERT: J 220 ARG cc_start: 0.8364 (mtt-85) cc_final: 0.7907 (mtt90) REVERT: J 289 ARG cc_start: 0.7969 (mmp-170) cc_final: 0.7693 (mmp-170) REVERT: J 312 PHE cc_start: 0.8357 (m-10) cc_final: 0.8113 (m-80) REVERT: J 388 ILE cc_start: 0.8866 (tp) cc_final: 0.8583 (tt) REVERT: J 408 ASN cc_start: 0.7892 (m-40) cc_final: 0.7406 (m-40) REVERT: K 3 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7973 (p) REVERT: K 35 TRP cc_start: 0.8787 (m-90) cc_final: 0.8344 (m-90) REVERT: K 36 ASP cc_start: 0.7997 (p0) cc_final: 0.7682 (p0) REVERT: K 40 ASP cc_start: 0.8121 (p0) cc_final: 0.7861 (p0) REVERT: K 74 ASP cc_start: 0.7614 (p0) cc_final: 0.7319 (p0) REVERT: K 81 GLU cc_start: 0.7857 (mp0) cc_final: 0.7612 (mp0) REVERT: K 151 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8249 (ttmm) REVERT: K 224 LYS cc_start: 0.8491 (ptmt) cc_final: 0.8055 (ptmt) REVERT: K 334 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8076 (mm-30) REVERT: L 37 LYS cc_start: 0.7874 (tmtt) cc_final: 0.7476 (tmtt) REVERT: L 62 ASP cc_start: 0.7821 (t0) cc_final: 0.7540 (t0) REVERT: L 79 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: L 149 LYS cc_start: 0.8425 (ptpt) cc_final: 0.8159 (ptpt) REVERT: A 15 TYR cc_start: 0.8114 (t80) cc_final: 0.7777 (t80) REVERT: A 45 GLU cc_start: 0.7961 (tp30) cc_final: 0.7646 (tp30) REVERT: A 131 VAL cc_start: 0.8654 (t) cc_final: 0.8273 (p) REVERT: A 192 TYR cc_start: 0.8664 (t80) cc_final: 0.8287 (t80) REVERT: A 202 ASP cc_start: 0.8133 (p0) cc_final: 0.7912 (p0) REVERT: A 226 VAL cc_start: 0.8686 (p) cc_final: 0.8457 (t) REVERT: A 262 GLU cc_start: 0.7915 (mp0) cc_final: 0.7171 (mp0) REVERT: A 264 GLU cc_start: 0.7644 (pm20) cc_final: 0.7303 (pm20) REVERT: A 365 PHE cc_start: 0.8212 (p90) cc_final: 0.7428 (p90) REVERT: A 379 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6815 (mm-30) REVERT: A 381 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8239 (mtmm) REVERT: A 433 MET cc_start: 0.7602 (mmm) cc_final: 0.7210 (mmm) REVERT: B 6 PHE cc_start: 0.8199 (m-80) cc_final: 0.7490 (m-80) REVERT: B 19 CYS cc_start: 0.7543 (m) cc_final: 0.7100 (m) REVERT: B 25 CYS cc_start: 0.6545 (p) cc_final: 0.6129 (p) REVERT: B 51 PHE cc_start: 0.8233 (m-80) cc_final: 0.8016 (m-80) REVERT: B 60 ASP cc_start: 0.7715 (t70) cc_final: 0.7507 (t70) REVERT: B 105 CYS cc_start: 0.8302 (m) cc_final: 0.7971 (m) REVERT: B 132 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8299 (mtm-85) REVERT: B 140 TYR cc_start: 0.8655 (p90) cc_final: 0.8408 (p90) REVERT: B 158 LEU cc_start: 0.8670 (tp) cc_final: 0.8453 (tt) REVERT: B 168 MET cc_start: 0.8132 (mmm) cc_final: 0.7897 (mmm) REVERT: B 176 TYR cc_start: 0.8163 (m-80) cc_final: 0.7924 (m-80) REVERT: B 177 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8054 (ttpp) REVERT: B 181 GLU cc_start: 0.7764 (tt0) cc_final: 0.7505 (tt0) REVERT: B 216 LYS cc_start: 0.8361 (tttm) cc_final: 0.8147 (tttm) REVERT: B 230 LYS cc_start: 0.8471 (mttm) cc_final: 0.8219 (mttm) REVERT: B 266 CYS cc_start: 0.7544 (m) cc_final: 0.7203 (m) REVERT: B 305 ASP cc_start: 0.7802 (m-30) cc_final: 0.7463 (m-30) REVERT: B 324 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 354 GLU cc_start: 0.7573 (mp0) cc_final: 0.7347 (mp0) REVERT: B 394 ARG cc_start: 0.8064 (mmp80) cc_final: 0.7856 (mmp80) REVERT: C 37 LYS cc_start: 0.8552 (tmtt) cc_final: 0.8328 (tmtt) outliers start: 140 outliers final: 114 residues processed: 1173 average time/residue: 0.4960 time to fit residues: 906.9582 Evaluate side-chains 1236 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1118 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 27 TYR Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 134 ASN Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 43 ASN Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 207 SER Chi-restraints excluded: chain J residue 280 ILE Chi-restraints excluded: chain J residue 291 SER Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 30 optimal weight: 0.0470 chunk 162 optimal weight: 0.0770 chunk 213 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 302 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 HIS D 319 GLN D 345 HIS ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 HIS G 408 ASN J 43 ASN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS C 89 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134525 restraints weight = 55811.419| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.74 r_work: 0.3335 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34608 Z= 0.126 Angle : 0.636 13.319 47157 Z= 0.318 Chirality : 0.047 0.259 5337 Planarity : 0.005 0.060 6017 Dihedral : 5.760 56.588 4997 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.54 % Favored : 94.44 % Rotamer: Outliers : 3.42 % Allowed : 16.92 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4280 helix: 1.41 (0.23), residues: 475 sheet: -0.40 (0.14), residues: 1256 loop : -1.16 (0.12), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 90 HIS 0.007 0.001 HIS B 363 PHE 0.019 0.001 PHE H 134 TYR 0.021 0.001 TYR D 320 ARG 0.010 0.001 ARG D 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 16) link_NAG-ASN : angle 2.30339 ( 48) hydrogen bonds : bond 0.03337 ( 1082) hydrogen bonds : angle 5.32040 ( 2859) SS BOND : bond 0.00321 ( 60) SS BOND : angle 1.61038 ( 120) covalent geometry : bond 0.00287 (34532) covalent geometry : angle 0.62787 (46989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1105 time to evaluate : 3.380 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: D 45 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7537 (tm-30) REVERT: D 104 SER cc_start: 0.7879 (m) cc_final: 0.7582 (p) REVERT: D 144 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8310 (pp) REVERT: D 264 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7554 (mm-30) REVERT: D 321 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7757 (mmtm) REVERT: D 324 ARG cc_start: 0.8449 (ttp-110) cc_final: 0.8157 (ttp-110) REVERT: D 325 GLU cc_start: 0.7522 (mp0) cc_final: 0.7305 (mp0) REVERT: D 406 SER cc_start: 0.8660 (t) cc_final: 0.8032 (p) REVERT: E 25 CYS cc_start: 0.5814 (t) cc_final: 0.4914 (p) REVERT: E 74 ASP cc_start: 0.7632 (p0) cc_final: 0.7396 (p0) REVERT: E 242 ASP cc_start: 0.7206 (t0) cc_final: 0.6892 (t0) REVERT: E 303 ARG cc_start: 0.7721 (ttt90) cc_final: 0.7174 (ttt90) REVERT: E 334 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7585 (mm-30) REVERT: E 354 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7246 (mt-10) REVERT: E 355 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7930 (mp) REVERT: E 388 CYS cc_start: 0.7997 (p) cc_final: 0.7435 (m) REVERT: F 8 MET cc_start: 0.6663 (mmm) cc_final: 0.6436 (mmm) REVERT: F 60 MET cc_start: 0.7689 (mmp) cc_final: 0.7463 (mmp) REVERT: G 99 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7016 (tm-30) REVERT: G 130 LYS cc_start: 0.8338 (ttmm) cc_final: 0.8138 (ttmm) REVERT: G 234 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8198 (p) REVERT: G 264 GLU cc_start: 0.7806 (mp0) cc_final: 0.7405 (mp0) REVERT: G 320 TYR cc_start: 0.8411 (p90) cc_final: 0.8128 (p90) REVERT: G 338 VAL cc_start: 0.8724 (p) cc_final: 0.8481 (t) REVERT: G 341 GLU cc_start: 0.8092 (mp0) cc_final: 0.7597 (mp0) REVERT: G 367 VAL cc_start: 0.8507 (t) cc_final: 0.8160 (p) REVERT: G 428 LEU cc_start: 0.8162 (mt) cc_final: 0.7576 (mt) REVERT: G 432 SER cc_start: 0.8341 (t) cc_final: 0.8114 (p) REVERT: H 36 ASP cc_start: 0.7335 (p0) cc_final: 0.6999 (p0) REVERT: H 37 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7466 (mm-30) REVERT: H 60 ASP cc_start: 0.7754 (t0) cc_final: 0.7379 (t0) REVERT: H 66 TYR cc_start: 0.8549 (p90) cc_final: 0.8212 (p90) REVERT: H 76 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8255 (mtmm) REVERT: H 78 ASP cc_start: 0.7905 (t0) cc_final: 0.7515 (t0) REVERT: H 82 LYS cc_start: 0.8142 (ptpt) cc_final: 0.7543 (ptpt) REVERT: H 151 LYS cc_start: 0.8649 (tttm) cc_final: 0.8407 (tttm) REVERT: H 168 MET cc_start: 0.7929 (mmm) cc_final: 0.7077 (mmm) REVERT: H 179 TYR cc_start: 0.7889 (m-10) cc_final: 0.7645 (m-10) REVERT: H 181 GLU cc_start: 0.6626 (mp0) cc_final: 0.5420 (mp0) REVERT: H 190 LYS cc_start: 0.7813 (mttm) cc_final: 0.7336 (mttm) REVERT: H 211 VAL cc_start: 0.7811 (m) cc_final: 0.7455 (p) REVERT: H 260 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7951 (ttp-170) REVERT: H 370 VAL cc_start: 0.7942 (t) cc_final: 0.7739 (p) REVERT: I 8 MET cc_start: 0.5059 (mmt) cc_final: 0.4756 (mmt) REVERT: I 19 MET cc_start: 0.7057 (tpt) cc_final: 0.6765 (tpt) REVERT: J 134 ARG cc_start: 0.7604 (ttp-110) cc_final: 0.7313 (ttp80) REVERT: J 220 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7706 (mtt90) REVERT: J 234 THR cc_start: 0.8582 (t) cc_final: 0.8327 (m) REVERT: J 241 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7338 (mm-30) REVERT: J 289 ARG cc_start: 0.7734 (mmp-170) cc_final: 0.7478 (mmp-170) REVERT: J 388 ILE cc_start: 0.8713 (tp) cc_final: 0.8430 (tt) REVERT: J 408 ASN cc_start: 0.7745 (m-40) cc_final: 0.7283 (m-40) REVERT: K 3 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7869 (p) REVERT: K 33 ASN cc_start: 0.8382 (m110) cc_final: 0.8115 (m110) REVERT: K 35 TRP cc_start: 0.8729 (m-90) cc_final: 0.8188 (m-90) REVERT: K 36 ASP cc_start: 0.7730 (p0) cc_final: 0.7427 (p0) REVERT: K 40 ASP cc_start: 0.7883 (p0) cc_final: 0.7667 (p0) REVERT: K 60 ASP cc_start: 0.7553 (t0) cc_final: 0.7034 (t0) REVERT: K 74 ASP cc_start: 0.7504 (p0) cc_final: 0.7219 (p0) REVERT: K 81 GLU cc_start: 0.7550 (mp0) cc_final: 0.7289 (mp0) REVERT: K 134 PHE cc_start: 0.7260 (m-80) cc_final: 0.6930 (m-10) REVERT: K 151 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8065 (ttmm) REVERT: K 206 TYR cc_start: 0.8110 (t80) cc_final: 0.7894 (t80) REVERT: K 224 LYS cc_start: 0.8330 (ptmt) cc_final: 0.7869 (ptmt) REVERT: K 334 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7745 (mm-30) REVERT: L 37 LYS cc_start: 0.7751 (tmtt) cc_final: 0.7375 (tmtt) REVERT: L 62 ASP cc_start: 0.7585 (t0) cc_final: 0.7367 (t0) REVERT: L 79 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: L 149 LYS cc_start: 0.8216 (ptpt) cc_final: 0.7935 (ptpt) REVERT: A 15 TYR cc_start: 0.7902 (t80) cc_final: 0.7571 (t80) REVERT: A 45 GLU cc_start: 0.7539 (tp30) cc_final: 0.7279 (tp30) REVERT: A 46 TYR cc_start: 0.8466 (p90) cc_final: 0.8034 (p90) REVERT: A 131 VAL cc_start: 0.8565 (t) cc_final: 0.8181 (p) REVERT: A 202 ASP cc_start: 0.7956 (p0) cc_final: 0.7687 (p0) REVERT: A 264 GLU cc_start: 0.7437 (pm20) cc_final: 0.7113 (pm20) REVERT: A 379 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6623 (mm-30) REVERT: A 381 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8092 (mtmm) REVERT: A 433 MET cc_start: 0.7438 (mmm) cc_final: 0.7025 (mmm) REVERT: B 6 PHE cc_start: 0.8113 (m-80) cc_final: 0.7763 (m-80) REVERT: B 19 CYS cc_start: 0.6885 (m) cc_final: 0.6337 (m) REVERT: B 25 CYS cc_start: 0.6055 (p) cc_final: 0.5609 (p) REVERT: B 132 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.8000 (mtm-85) REVERT: B 158 LEU cc_start: 0.8649 (tp) cc_final: 0.8424 (tt) REVERT: B 168 MET cc_start: 0.7747 (mmm) cc_final: 0.7514 (mmm) REVERT: B 177 LYS cc_start: 0.8204 (ttpp) cc_final: 0.7820 (ttpp) REVERT: B 199 TYR cc_start: 0.6407 (p90) cc_final: 0.5223 (p90) REVERT: B 216 LYS cc_start: 0.8132 (tttm) cc_final: 0.7877 (tttm) REVERT: B 230 LYS cc_start: 0.8354 (mttm) cc_final: 0.8074 (mttm) REVERT: B 305 ASP cc_start: 0.7507 (m-30) cc_final: 0.7151 (m-30) REVERT: B 324 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 394 ARG cc_start: 0.7890 (mmp80) cc_final: 0.7665 (mmp80) REVERT: C 16 PHE cc_start: 0.7382 (m-10) cc_final: 0.7174 (m-10) REVERT: C 37 LYS cc_start: 0.8348 (tmtt) cc_final: 0.8023 (tmtt) outliers start: 126 outliers final: 90 residues processed: 1143 average time/residue: 0.5041 time to fit residues: 900.0004 Evaluate side-chains 1189 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1093 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 GLN Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 91 HIS Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 94 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 404 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 381 optimal weight: 9.9990 chunk 295 optimal weight: 20.0000 chunk 206 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 ASN G 408 ASN H 46 GLN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118054 restraints weight = 56324.916| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.68 r_work: 0.3274 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 34608 Z= 0.296 Angle : 0.710 12.461 47157 Z= 0.361 Chirality : 0.050 0.240 5337 Planarity : 0.005 0.063 6017 Dihedral : 5.994 56.220 4997 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.06 % Favored : 92.92 % Rotamer: Outliers : 4.23 % Allowed : 16.86 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 4280 helix: 1.45 (0.23), residues: 466 sheet: -0.52 (0.14), residues: 1250 loop : -1.25 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 90 HIS 0.007 0.001 HIS B 353 PHE 0.034 0.002 PHE K 134 TYR 0.032 0.002 TYR D 320 ARG 0.011 0.001 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 16) link_NAG-ASN : angle 2.55389 ( 48) hydrogen bonds : bond 0.03825 ( 1082) hydrogen bonds : angle 5.47355 ( 2859) SS BOND : bond 0.00460 ( 60) SS BOND : angle 1.92679 ( 120) covalent geometry : bond 0.00660 (34532) covalent geometry : angle 0.69937 (46989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1282 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1126 time to evaluate : 3.755 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: D 45 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7454 (tm-30) REVERT: D 104 SER cc_start: 0.7934 (m) cc_final: 0.7615 (p) REVERT: D 321 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7791 (mmtm) REVERT: D 324 ARG cc_start: 0.8517 (ttp-110) cc_final: 0.8226 (ttp-110) REVERT: D 372 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7828 (ptpp) REVERT: D 406 SER cc_start: 0.8648 (t) cc_final: 0.8011 (p) REVERT: E 74 ASP cc_start: 0.7676 (p0) cc_final: 0.7413 (p0) REVERT: E 189 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7605 (mp) REVERT: E 200 GLU cc_start: 0.7099 (tt0) cc_final: 0.6666 (tt0) REVERT: E 242 ASP cc_start: 0.7163 (t70) cc_final: 0.6840 (t0) REVERT: E 303 ARG cc_start: 0.7711 (ttt90) cc_final: 0.7181 (ttt90) REVERT: E 334 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7600 (mm-30) REVERT: E 354 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7362 (mt-10) REVERT: E 355 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7945 (mp) REVERT: F 8 MET cc_start: 0.6697 (mmm) cc_final: 0.6357 (mmm) REVERT: F 60 MET cc_start: 0.7830 (mmp) cc_final: 0.7602 (mmp) REVERT: G 99 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7139 (tm-30) REVERT: G 130 LYS cc_start: 0.8382 (ttmm) cc_final: 0.8115 (ttmm) REVERT: G 264 GLU cc_start: 0.7767 (mp0) cc_final: 0.7428 (mp0) REVERT: G 287 PHE cc_start: 0.7841 (m-80) cc_final: 0.7568 (m-80) REVERT: G 324 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7554 (mtm110) REVERT: G 338 VAL cc_start: 0.8733 (p) cc_final: 0.8499 (t) REVERT: G 341 GLU cc_start: 0.8179 (mp0) cc_final: 0.7666 (mp0) REVERT: G 367 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8207 (p) REVERT: G 404 LYS cc_start: 0.8410 (tppp) cc_final: 0.7951 (tppp) REVERT: G 428 LEU cc_start: 0.8186 (mt) cc_final: 0.7592 (mt) REVERT: G 432 SER cc_start: 0.8299 (t) cc_final: 0.8085 (p) REVERT: H 36 ASP cc_start: 0.7363 (p0) cc_final: 0.7038 (p0) REVERT: H 37 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7483 (mm-30) REVERT: H 60 ASP cc_start: 0.7859 (t0) cc_final: 0.7504 (t0) REVERT: H 76 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8332 (mtmm) REVERT: H 78 ASP cc_start: 0.7863 (t0) cc_final: 0.7523 (t0) REVERT: H 82 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7654 (ptpt) REVERT: H 151 LYS cc_start: 0.8619 (tttm) cc_final: 0.8370 (tttm) REVERT: H 168 MET cc_start: 0.8009 (mmm) cc_final: 0.7138 (mmm) REVERT: H 179 TYR cc_start: 0.8031 (m-10) cc_final: 0.7794 (m-10) REVERT: H 211 VAL cc_start: 0.7850 (m) cc_final: 0.7508 (p) REVERT: H 260 ARG cc_start: 0.8251 (ttp-110) cc_final: 0.7974 (ttp-170) REVERT: H 391 LYS cc_start: 0.7837 (tppp) cc_final: 0.7453 (tppp) REVERT: I 8 MET cc_start: 0.5134 (mmt) cc_final: 0.4859 (mmt) REVERT: J 76 TYR cc_start: 0.8386 (t80) cc_final: 0.8022 (t80) REVERT: J 105 GLU cc_start: 0.7540 (mt-10) cc_final: 0.6955 (mt-10) REVERT: J 134 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7305 (ttp80) REVERT: J 220 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7701 (mtt90) REVERT: J 241 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7350 (mm-30) REVERT: J 289 ARG cc_start: 0.7708 (mmp-170) cc_final: 0.7473 (mmp-170) REVERT: J 388 ILE cc_start: 0.8810 (tp) cc_final: 0.8530 (tt) REVERT: J 408 ASN cc_start: 0.7781 (m-40) cc_final: 0.7266 (m-40) REVERT: K 20 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7478 (ttt180) REVERT: K 35 TRP cc_start: 0.8737 (m-90) cc_final: 0.8288 (m-90) REVERT: K 36 ASP cc_start: 0.7749 (p0) cc_final: 0.7525 (p0) REVERT: K 60 ASP cc_start: 0.7560 (t0) cc_final: 0.7050 (t0) REVERT: K 74 ASP cc_start: 0.7506 (p0) cc_final: 0.7211 (p0) REVERT: K 81 GLU cc_start: 0.7604 (mp0) cc_final: 0.7356 (mp0) REVERT: K 134 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7195 (m-10) REVERT: K 151 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8105 (ttmm) REVERT: K 224 LYS cc_start: 0.8437 (ptmt) cc_final: 0.7969 (ptmt) REVERT: K 334 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7791 (mm-30) REVERT: L 37 LYS cc_start: 0.7821 (tmtt) cc_final: 0.7462 (tmtt) REVERT: L 62 ASP cc_start: 0.7688 (t0) cc_final: 0.7438 (t0) REVERT: L 79 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: L 149 LYS cc_start: 0.8233 (ptpt) cc_final: 0.7962 (ptpt) REVERT: A 15 TYR cc_start: 0.7983 (t80) cc_final: 0.7631 (t80) REVERT: A 46 TYR cc_start: 0.8510 (p90) cc_final: 0.8030 (p90) REVERT: A 131 VAL cc_start: 0.8554 (t) cc_final: 0.8177 (p) REVERT: A 202 ASP cc_start: 0.7968 (p0) cc_final: 0.7713 (p0) REVERT: A 226 VAL cc_start: 0.8603 (p) cc_final: 0.8384 (t) REVERT: A 264 GLU cc_start: 0.7484 (pm20) cc_final: 0.7222 (pm20) REVERT: A 365 PHE cc_start: 0.8107 (p90) cc_final: 0.7520 (p90) REVERT: A 379 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6599 (mm-30) REVERT: A 381 LYS cc_start: 0.8367 (mtmm) cc_final: 0.8102 (mtmm) REVERT: A 433 MET cc_start: 0.7490 (mmm) cc_final: 0.7215 (mmm) REVERT: B 6 PHE cc_start: 0.8135 (m-80) cc_final: 0.7742 (m-80) REVERT: B 19 CYS cc_start: 0.6976 (m) cc_final: 0.6425 (m) REVERT: B 25 CYS cc_start: 0.6059 (p) cc_final: 0.5623 (p) REVERT: B 74 ASP cc_start: 0.7205 (p0) cc_final: 0.6918 (p0) REVERT: B 105 CYS cc_start: 0.7936 (m) cc_final: 0.7611 (m) REVERT: B 132 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7977 (mtm-85) REVERT: B 168 MET cc_start: 0.7828 (mmm) cc_final: 0.7609 (mmm) REVERT: B 177 LYS cc_start: 0.8296 (ttpp) cc_final: 0.7974 (ttpp) REVERT: B 216 LYS cc_start: 0.8295 (tttm) cc_final: 0.8031 (tttm) REVERT: B 230 LYS cc_start: 0.8362 (mttm) cc_final: 0.8077 (mttm) REVERT: B 266 CYS cc_start: 0.6956 (m) cc_final: 0.6530 (m) REVERT: B 305 ASP cc_start: 0.7505 (m-30) cc_final: 0.7162 (m-30) REVERT: B 324 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 37 LYS cc_start: 0.8360 (tmtt) cc_final: 0.8143 (tmtt) outliers start: 156 outliers final: 124 residues processed: 1181 average time/residue: 0.4933 time to fit residues: 906.9182 Evaluate side-chains 1253 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1121 time to evaluate : 5.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 GLN Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 280 ILE Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 134 PHE Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain K residue 290 THR Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 191 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 402 optimal weight: 6.9990 chunk 136 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 322 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 235 optimal weight: 0.8980 chunk 426 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 52 HIS D 319 GLN ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 102 GLN G 196 ASN G 408 ASN H 122 ASN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 HIS ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** 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 = 0.3718 r_free = 0.3718 target = 0.139412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119160 restraints weight = 56651.678| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.70 r_work: 0.3292 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34608 Z= 0.198 Angle : 0.679 14.017 47157 Z= 0.342 Chirality : 0.048 0.361 5337 Planarity : 0.005 0.063 6017 Dihedral : 5.879 56.470 4997 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.82 % Favored : 94.16 % Rotamer: Outliers : 3.88 % Allowed : 18.41 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4280 helix: 1.53 (0.23), residues: 466 sheet: -0.47 (0.14), residues: 1269 loop : -1.22 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 90 HIS 0.007 0.001 HIS K 169 PHE 0.029 0.002 PHE H 134 TYR 0.036 0.002 TYR D 320 ARG 0.012 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 16) link_NAG-ASN : angle 2.40729 ( 48) hydrogen bonds : bond 0.03521 ( 1082) hydrogen bonds : angle 5.38651 ( 2859) SS BOND : bond 0.00390 ( 60) SS BOND : angle 2.05405 ( 120) covalent geometry : bond 0.00446 (34532) covalent geometry : angle 0.66805 (46989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1112 time to evaluate : 3.556 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: D 45 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7480 (tm-30) REVERT: D 104 SER cc_start: 0.7911 (m) cc_final: 0.7609 (p) REVERT: D 144 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8252 (pp) REVERT: D 160 LYS cc_start: 0.8075 (tttm) cc_final: 0.7693 (mttm) REVERT: D 264 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7519 (mm-30) REVERT: D 321 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7804 (mmtm) REVERT: D 324 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.8215 (ttp-110) REVERT: D 372 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7814 (pttm) REVERT: D 406 SER cc_start: 0.8636 (t) cc_final: 0.8000 (p) REVERT: E 74 ASP cc_start: 0.7702 (p0) cc_final: 0.7450 (p0) REVERT: E 189 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7488 (mp) REVERT: E 242 ASP cc_start: 0.7196 (t70) cc_final: 0.6822 (t0) REVERT: E 303 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7168 (ttt90) REVERT: E 334 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7582 (mm-30) REVERT: E 354 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7279 (mt-10) REVERT: E 355 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7922 (mp) REVERT: F 8 MET cc_start: 0.6731 (mmm) cc_final: 0.6362 (mmm) REVERT: F 60 MET cc_start: 0.7759 (mmp) cc_final: 0.7517 (mmp) REVERT: G 61 LYS cc_start: 0.7436 (tptm) cc_final: 0.7203 (tptm) REVERT: G 99 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7078 (tm-30) REVERT: G 130 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8188 (ttmm) REVERT: G 234 THR cc_start: 0.8434 (p) cc_final: 0.8217 (p) REVERT: G 264 GLU cc_start: 0.7767 (mp0) cc_final: 0.7405 (mp0) REVERT: G 287 PHE cc_start: 0.7837 (m-80) cc_final: 0.7585 (m-80) REVERT: G 338 VAL cc_start: 0.8728 (p) cc_final: 0.8489 (t) REVERT: G 341 GLU cc_start: 0.8165 (mp0) cc_final: 0.7658 (mp0) REVERT: G 367 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8160 (p) REVERT: G 404 LYS cc_start: 0.8402 (tppp) cc_final: 0.7965 (tppp) REVERT: G 428 LEU cc_start: 0.8176 (mt) cc_final: 0.7588 (mt) REVERT: G 432 SER cc_start: 0.8356 (t) cc_final: 0.8134 (p) REVERT: H 36 ASP cc_start: 0.7332 (p0) cc_final: 0.7022 (p0) REVERT: H 60 ASP cc_start: 0.7796 (t0) cc_final: 0.7448 (t0) REVERT: H 65 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7165 (mtp180) REVERT: H 76 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8335 (mtmm) REVERT: H 78 ASP cc_start: 0.7897 (t0) cc_final: 0.7542 (t0) REVERT: H 82 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7585 (ptpt) REVERT: H 151 LYS cc_start: 0.8643 (tttm) cc_final: 0.8387 (tttm) REVERT: H 159 LYS cc_start: 0.8708 (pttm) cc_final: 0.8504 (pttm) REVERT: H 168 MET cc_start: 0.7999 (mmm) cc_final: 0.7142 (mmm) REVERT: H 181 GLU cc_start: 0.6372 (mp0) cc_final: 0.5777 (mp0) REVERT: H 211 VAL cc_start: 0.7824 (m) cc_final: 0.7458 (p) REVERT: H 260 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7967 (ttp-170) REVERT: H 391 LYS cc_start: 0.7846 (tppp) cc_final: 0.7441 (tppp) REVERT: I 8 MET cc_start: 0.5056 (mmt) cc_final: 0.4787 (mmt) REVERT: I 97 TYR cc_start: 0.5802 (t80) cc_final: 0.5459 (t80) REVERT: J 76 TYR cc_start: 0.8372 (t80) cc_final: 0.8117 (t80) REVERT: J 105 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7058 (mt-10) REVERT: J 134 ARG cc_start: 0.7608 (ttp-110) cc_final: 0.7268 (ttp80) REVERT: J 220 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7657 (mtt90) REVERT: J 241 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7306 (mm-30) REVERT: J 289 ARG cc_start: 0.7691 (mmp-170) cc_final: 0.7418 (mmp-170) REVERT: J 388 ILE cc_start: 0.8775 (tp) cc_final: 0.8506 (tt) REVERT: J 408 ASN cc_start: 0.7783 (m-40) cc_final: 0.7289 (m-40) REVERT: K 20 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7368 (ttt180) REVERT: K 35 TRP cc_start: 0.8745 (m-90) cc_final: 0.8231 (m-90) REVERT: K 36 ASP cc_start: 0.7752 (p0) cc_final: 0.7511 (p0) REVERT: K 60 ASP cc_start: 0.7552 (t0) cc_final: 0.7028 (t0) REVERT: K 74 ASP cc_start: 0.7483 (p0) cc_final: 0.7185 (p0) REVERT: K 81 GLU cc_start: 0.7598 (mp0) cc_final: 0.7302 (mp0) REVERT: K 134 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: K 151 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8055 (ttmm) REVERT: K 224 LYS cc_start: 0.8384 (ptmt) cc_final: 0.7913 (ptmt) REVERT: K 334 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7778 (mm-30) REVERT: L 37 LYS cc_start: 0.7818 (tmtt) cc_final: 0.7487 (tmtt) REVERT: L 62 ASP cc_start: 0.7674 (t0) cc_final: 0.7443 (t0) REVERT: L 79 TYR cc_start: 0.7622 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: L 149 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7978 (ptpt) REVERT: A 46 TYR cc_start: 0.8492 (p90) cc_final: 0.7991 (p90) REVERT: A 105 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7454 (mt-10) REVERT: A 131 VAL cc_start: 0.8581 (t) cc_final: 0.8219 (p) REVERT: A 202 ASP cc_start: 0.7982 (p0) cc_final: 0.7701 (p0) REVERT: A 264 GLU cc_start: 0.7486 (pm20) cc_final: 0.7266 (pm20) REVERT: A 365 PHE cc_start: 0.8032 (p90) cc_final: 0.7536 (p90) REVERT: A 379 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6581 (mm-30) REVERT: A 381 LYS cc_start: 0.8355 (mtmm) cc_final: 0.8092 (mtmm) REVERT: A 433 MET cc_start: 0.7480 (mmm) cc_final: 0.7190 (mmm) REVERT: B 6 PHE cc_start: 0.8049 (m-80) cc_final: 0.7737 (m-80) REVERT: B 19 CYS cc_start: 0.6972 (m) cc_final: 0.6442 (m) REVERT: B 25 CYS cc_start: 0.6092 (p) cc_final: 0.5657 (p) REVERT: B 132 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7967 (mtm-85) REVERT: B 168 MET cc_start: 0.7818 (mmm) cc_final: 0.7590 (mmm) REVERT: B 177 LYS cc_start: 0.8292 (ttpp) cc_final: 0.7950 (ttpp) REVERT: B 181 GLU cc_start: 0.7689 (tt0) cc_final: 0.7476 (tt0) REVERT: B 216 LYS cc_start: 0.8274 (tttm) cc_final: 0.7996 (tttm) REVERT: B 230 LYS cc_start: 0.8364 (mttm) cc_final: 0.8069 (mttm) REVERT: B 266 CYS cc_start: 0.6609 (m) cc_final: 0.6167 (m) REVERT: B 305 ASP cc_start: 0.7513 (m-30) cc_final: 0.7159 (m-30) REVERT: B 324 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 394 ARG cc_start: 0.7610 (mmp80) cc_final: 0.7159 (mmp80) REVERT: C 37 LYS cc_start: 0.8384 (tmtt) cc_final: 0.8057 (tmtt) outliers start: 143 outliers final: 119 residues processed: 1162 average time/residue: 0.5160 time to fit residues: 933.7963 Evaluate side-chains 1245 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1116 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 319 GLN Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 311 ASP Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 43 ASN Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 280 ILE Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 134 PHE Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 26 optimal weight: 3.9990 chunk 282 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 406 optimal weight: 8.9990 chunk 293 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 354 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 319 GLN E 21 HIS ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 408 ASN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.139896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119731 restraints weight = 56196.790| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.69 r_work: 0.3296 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34608 Z= 0.176 Angle : 0.669 13.673 47157 Z= 0.335 Chirality : 0.048 0.278 5337 Planarity : 0.005 0.062 6017 Dihedral : 5.818 56.377 4997 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.60 % Rotamer: Outliers : 4.04 % Allowed : 18.70 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4280 helix: 1.58 (0.24), residues: 466 sheet: -0.46 (0.14), residues: 1273 loop : -1.22 (0.12), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 90 HIS 0.007 0.001 HIS K 169 PHE 0.028 0.002 PHE H 134 TYR 0.036 0.002 TYR D 320 ARG 0.011 0.001 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 16) link_NAG-ASN : angle 2.34946 ( 48) hydrogen bonds : bond 0.03439 ( 1082) hydrogen bonds : angle 5.31510 ( 2859) SS BOND : bond 0.00359 ( 60) SS BOND : angle 1.78820 ( 120) covalent geometry : bond 0.00399 (34532) covalent geometry : angle 0.65946 (46989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1114 time to evaluate : 3.546 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: D 45 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: D 104 SER cc_start: 0.7989 (m) cc_final: 0.7703 (p) REVERT: D 144 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8326 (pp) REVERT: D 160 LYS cc_start: 0.8157 (tttm) cc_final: 0.7777 (mttm) REVERT: D 264 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7809 (mm-30) REVERT: D 289 ARG cc_start: 0.8241 (tpt170) cc_final: 0.7634 (tpt170) REVERT: D 321 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7941 (mmtm) REVERT: D 324 ARG cc_start: 0.8611 (ttp-110) cc_final: 0.8342 (ttp-110) REVERT: D 406 SER cc_start: 0.8722 (t) cc_final: 0.8123 (p) REVERT: E 74 ASP cc_start: 0.7921 (p0) cc_final: 0.7679 (p0) REVERT: E 168 MET cc_start: 0.7956 (mmm) cc_final: 0.7412 (mmm) REVERT: E 189 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7551 (mp) REVERT: E 200 GLU cc_start: 0.7260 (tt0) cc_final: 0.6876 (tt0) REVERT: E 230 LYS cc_start: 0.8440 (mttt) cc_final: 0.8183 (mttt) REVERT: E 242 ASP cc_start: 0.7410 (t70) cc_final: 0.7050 (t0) REVERT: E 303 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7361 (ttt90) REVERT: E 334 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7887 (mm-30) REVERT: E 354 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7409 (mt-10) REVERT: E 355 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8055 (mp) REVERT: F 8 MET cc_start: 0.6990 (mmm) cc_final: 0.6551 (mmm) REVERT: F 60 MET cc_start: 0.8170 (mmp) cc_final: 0.7894 (mmp) REVERT: G 9 ASN cc_start: 0.7822 (t160) cc_final: 0.7593 (t0) REVERT: G 61 LYS cc_start: 0.7547 (tptm) cc_final: 0.7329 (tptm) REVERT: G 99 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7208 (tm-30) REVERT: G 130 LYS cc_start: 0.8594 (ttmm) cc_final: 0.8393 (ttmm) REVERT: G 234 THR cc_start: 0.8517 (p) cc_final: 0.8306 (p) REVERT: G 264 GLU cc_start: 0.7990 (mp0) cc_final: 0.7610 (mp0) REVERT: G 287 PHE cc_start: 0.7948 (m-80) cc_final: 0.7707 (m-80) REVERT: G 338 VAL cc_start: 0.8837 (p) cc_final: 0.8599 (t) REVERT: G 341 GLU cc_start: 0.8277 (mp0) cc_final: 0.7781 (mp0) REVERT: G 367 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8276 (p) REVERT: G 404 LYS cc_start: 0.8509 (tppp) cc_final: 0.8261 (tppp) REVERT: G 428 LEU cc_start: 0.8206 (mt) cc_final: 0.7624 (mt) REVERT: G 432 SER cc_start: 0.8406 (t) cc_final: 0.8174 (p) REVERT: H 36 ASP cc_start: 0.7439 (p0) cc_final: 0.7192 (p0) REVERT: H 60 ASP cc_start: 0.7962 (t0) cc_final: 0.7562 (t0) REVERT: H 65 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7314 (mtp180) REVERT: H 76 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8440 (mtmm) REVERT: H 78 ASP cc_start: 0.8145 (t0) cc_final: 0.7774 (t0) REVERT: H 82 LYS cc_start: 0.8261 (ptpt) cc_final: 0.7691 (ptpt) REVERT: H 151 LYS cc_start: 0.8778 (tttm) cc_final: 0.8529 (tttm) REVERT: H 168 MET cc_start: 0.8254 (mmm) cc_final: 0.7392 (mmm) REVERT: H 179 TYR cc_start: 0.8128 (m-10) cc_final: 0.7913 (m-10) REVERT: H 181 GLU cc_start: 0.6515 (mp0) cc_final: 0.5796 (mp0) REVERT: H 190 LYS cc_start: 0.7986 (tttm) cc_final: 0.7773 (mttm) REVERT: H 211 VAL cc_start: 0.7928 (m) cc_final: 0.7602 (p) REVERT: H 260 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.8211 (ttp-170) REVERT: H 391 LYS cc_start: 0.7908 (tppp) cc_final: 0.7518 (tppp) REVERT: I 8 MET cc_start: 0.5296 (mmt) cc_final: 0.4961 (mmt) REVERT: J 105 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7430 (mt-10) REVERT: J 134 ARG cc_start: 0.7718 (ttp-110) cc_final: 0.7353 (ttp80) REVERT: J 220 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.7902 (mtt90) REVERT: J 241 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7714 (mm-30) REVERT: J 289 ARG cc_start: 0.7956 (mmp-170) cc_final: 0.7635 (mmp-170) REVERT: J 388 ILE cc_start: 0.8842 (tp) cc_final: 0.8590 (tt) REVERT: J 408 ASN cc_start: 0.7854 (m-40) cc_final: 0.7379 (m-40) REVERT: K 20 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7644 (ttt180) REVERT: K 35 TRP cc_start: 0.8800 (m-90) cc_final: 0.8335 (m-90) REVERT: K 36 ASP cc_start: 0.7969 (p0) cc_final: 0.7643 (p0) REVERT: K 60 ASP cc_start: 0.7801 (t0) cc_final: 0.7273 (t0) REVERT: K 74 ASP cc_start: 0.7638 (p0) cc_final: 0.7356 (p0) REVERT: K 81 GLU cc_start: 0.7913 (mp0) cc_final: 0.7616 (mp0) REVERT: K 134 PHE cc_start: 0.7474 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: K 151 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8182 (ttmm) REVERT: K 224 LYS cc_start: 0.8471 (ptmt) cc_final: 0.8025 (ptmt) REVERT: K 334 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8098 (mm-30) REVERT: L 37 LYS cc_start: 0.7902 (tmtt) cc_final: 0.7593 (tmtt) REVERT: L 62 ASP cc_start: 0.7835 (t0) cc_final: 0.7545 (t0) REVERT: L 79 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6795 (m-80) REVERT: L 149 LYS cc_start: 0.8360 (ptpt) cc_final: 0.8123 (ptpt) REVERT: A 46 TYR cc_start: 0.8585 (p90) cc_final: 0.8044 (p90) REVERT: A 105 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7802 (mt-10) REVERT: A 131 VAL cc_start: 0.8676 (t) cc_final: 0.8340 (p) REVERT: A 134 ARG cc_start: 0.7736 (ttp-110) cc_final: 0.7347 (ttp-110) REVERT: A 264 GLU cc_start: 0.7704 (pm20) cc_final: 0.7441 (pm20) REVERT: A 365 PHE cc_start: 0.8108 (p90) cc_final: 0.7649 (p90) REVERT: A 379 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6778 (mm-30) REVERT: A 381 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8209 (mtmm) REVERT: A 433 MET cc_start: 0.7672 (mmm) cc_final: 0.7349 (mmm) REVERT: B 6 PHE cc_start: 0.8033 (m-80) cc_final: 0.7783 (m-80) REVERT: B 19 CYS cc_start: 0.7536 (m) cc_final: 0.7152 (m) REVERT: B 25 CYS cc_start: 0.6562 (p) cc_final: 0.6210 (p) REVERT: B 132 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8271 (mtm-85) REVERT: B 168 MET cc_start: 0.8098 (mmm) cc_final: 0.7855 (mmm) REVERT: B 177 LYS cc_start: 0.8368 (ttpp) cc_final: 0.8049 (ttpp) REVERT: B 181 GLU cc_start: 0.7862 (tt0) cc_final: 0.7637 (tt0) REVERT: B 216 LYS cc_start: 0.8301 (tttm) cc_final: 0.8037 (tttm) REVERT: B 230 LYS cc_start: 0.8445 (mttm) cc_final: 0.8169 (mttm) REVERT: B 305 ASP cc_start: 0.7811 (m-30) cc_final: 0.7461 (m-30) REVERT: B 324 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7771 (mt-10) REVERT: B 394 ARG cc_start: 0.7860 (mmp80) cc_final: 0.7373 (mmp80) outliers start: 149 outliers final: 122 residues processed: 1169 average time/residue: 0.6063 time to fit residues: 1106.7553 Evaluate side-chains 1243 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1111 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 319 GLN Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 280 ILE Chi-restraints excluded: chain J residue 324 ARG Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 134 PHE Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 355 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 342 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 346 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 chunk 388 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 ASN G 100 ASN G 408 ASN ** I 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.138710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118636 restraints weight = 56561.438| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.68 r_work: 0.3285 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34608 Z= 0.238 Angle : 0.708 13.721 47157 Z= 0.357 Chirality : 0.049 0.283 5337 Planarity : 0.005 0.062 6017 Dihedral : 5.939 56.276 4997 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.64 % Favored : 93.34 % Rotamer: Outliers : 4.12 % Allowed : 19.25 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.13), residues: 4280 helix: 1.53 (0.23), residues: 466 sheet: -0.49 (0.15), residues: 1248 loop : -1.26 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 90 HIS 0.007 0.001 HIS K 169 PHE 0.028 0.002 PHE H 134 TYR 0.034 0.002 TYR D 320 ARG 0.011 0.001 ARG A 220 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 16) link_NAG-ASN : angle 2.42160 ( 48) hydrogen bonds : bond 0.03624 ( 1082) hydrogen bonds : angle 5.38547 ( 2859) SS BOND : bond 0.00408 ( 60) SS BOND : angle 2.10901 ( 120) covalent geometry : bond 0.00535 (34532) covalent geometry : angle 0.69682 (46989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1115 time to evaluate : 3.554 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: D 45 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: D 104 SER cc_start: 0.8007 (m) cc_final: 0.7709 (p) REVERT: D 160 LYS cc_start: 0.8175 (tttm) cc_final: 0.7811 (mttm) REVERT: D 264 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7812 (mm-30) REVERT: D 289 ARG cc_start: 0.8261 (tpt170) cc_final: 0.7664 (tpt170) REVERT: D 321 LYS cc_start: 0.8300 (mmtm) cc_final: 0.7949 (mmtm) REVERT: D 324 ARG cc_start: 0.8639 (ttp-110) cc_final: 0.8428 (ttp-110) REVERT: D 406 SER cc_start: 0.8706 (t) cc_final: 0.8100 (p) REVERT: E 39 ASP cc_start: 0.8368 (m-30) cc_final: 0.8064 (m-30) REVERT: E 74 ASP cc_start: 0.7861 (p0) cc_final: 0.7525 (p0) REVERT: E 168 MET cc_start: 0.7989 (mmm) cc_final: 0.7449 (mmm) REVERT: E 189 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7611 (mp) REVERT: E 200 GLU cc_start: 0.7317 (tt0) cc_final: 0.6913 (tt0) REVERT: E 230 LYS cc_start: 0.8436 (mttt) cc_final: 0.8176 (mttt) REVERT: E 242 ASP cc_start: 0.7413 (t70) cc_final: 0.7056 (t0) REVERT: E 303 ARG cc_start: 0.7969 (ttt90) cc_final: 0.7375 (ttt90) REVERT: E 334 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7879 (mm-30) REVERT: E 354 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7526 (mt-10) REVERT: E 355 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8078 (mp) REVERT: F 8 MET cc_start: 0.7011 (mmm) cc_final: 0.6597 (mmm) REVERT: F 60 MET cc_start: 0.8168 (mmp) cc_final: 0.7900 (mmp) REVERT: G 9 ASN cc_start: 0.7884 (t0) cc_final: 0.7593 (t0) REVERT: G 99 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7236 (tm-30) REVERT: G 130 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8390 (ttmm) REVERT: G 262 GLU cc_start: 0.7728 (mp0) cc_final: 0.7383 (mp0) REVERT: G 264 GLU cc_start: 0.7994 (mp0) cc_final: 0.7643 (mp0) REVERT: G 287 PHE cc_start: 0.7959 (m-80) cc_final: 0.7720 (m-80) REVERT: G 321 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7739 (mmmt) REVERT: G 338 VAL cc_start: 0.8848 (p) cc_final: 0.8620 (t) REVERT: G 341 GLU cc_start: 0.8295 (mp0) cc_final: 0.7782 (mp0) REVERT: G 367 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8288 (p) REVERT: G 404 LYS cc_start: 0.8494 (tppp) cc_final: 0.8231 (tppp) REVERT: G 428 LEU cc_start: 0.8216 (mt) cc_final: 0.7639 (mt) REVERT: G 432 SER cc_start: 0.8360 (t) cc_final: 0.8144 (p) REVERT: H 36 ASP cc_start: 0.7469 (p0) cc_final: 0.7178 (p0) REVERT: H 60 ASP cc_start: 0.7968 (t0) cc_final: 0.7562 (t0) REVERT: H 65 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7309 (mtp180) REVERT: H 76 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8473 (mtmm) REVERT: H 78 ASP cc_start: 0.8131 (t0) cc_final: 0.7767 (t0) REVERT: H 82 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7705 (ptpt) REVERT: H 151 LYS cc_start: 0.8781 (tttm) cc_final: 0.8532 (tttm) REVERT: H 168 MET cc_start: 0.8257 (mmm) cc_final: 0.7416 (mmm) REVERT: H 179 TYR cc_start: 0.8291 (m-10) cc_final: 0.8085 (m-10) REVERT: H 181 GLU cc_start: 0.6511 (mp0) cc_final: 0.5814 (mp0) REVERT: H 190 LYS cc_start: 0.8101 (tttm) cc_final: 0.7860 (mttm) REVERT: H 211 VAL cc_start: 0.7937 (m) cc_final: 0.7607 (p) REVERT: H 260 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.8233 (ttp-170) REVERT: H 391 LYS cc_start: 0.7937 (tppp) cc_final: 0.7598 (tppp) REVERT: I 8 MET cc_start: 0.5174 (mmt) cc_final: 0.4890 (mmt) REVERT: J 134 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7364 (ttp80) REVERT: J 220 ARG cc_start: 0.8297 (mtt-85) cc_final: 0.7864 (mtt90) REVERT: J 234 THR cc_start: 0.8705 (t) cc_final: 0.8431 (m) REVERT: J 241 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7691 (mm-30) REVERT: J 289 ARG cc_start: 0.7942 (mmp-170) cc_final: 0.7615 (mmp-170) REVERT: J 408 ASN cc_start: 0.7856 (m-40) cc_final: 0.7366 (m-40) REVERT: K 20 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7665 (ttt180) REVERT: K 35 TRP cc_start: 0.8802 (m-90) cc_final: 0.8339 (m-90) REVERT: K 36 ASP cc_start: 0.7996 (p0) cc_final: 0.7666 (p0) REVERT: K 60 ASP cc_start: 0.7781 (t0) cc_final: 0.7247 (t0) REVERT: K 74 ASP cc_start: 0.7628 (p0) cc_final: 0.7320 (p0) REVERT: K 81 GLU cc_start: 0.7935 (mp0) cc_final: 0.7634 (mp0) REVERT: K 134 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: K 151 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8192 (ttmm) REVERT: K 224 LYS cc_start: 0.8488 (ptmt) cc_final: 0.8044 (ptmt) REVERT: K 334 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8099 (mm-30) REVERT: L 37 LYS cc_start: 0.7844 (tmtt) cc_final: 0.7553 (tmtt) REVERT: L 62 ASP cc_start: 0.7810 (t0) cc_final: 0.7506 (t0) REVERT: L 79 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: L 149 LYS cc_start: 0.8401 (ptpt) cc_final: 0.8162 (ptpt) REVERT: A 105 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7806 (mt-10) REVERT: A 131 VAL cc_start: 0.8676 (t) cc_final: 0.8348 (p) REVERT: A 134 ARG cc_start: 0.7739 (ttp-110) cc_final: 0.7353 (ttp-110) REVERT: A 264 GLU cc_start: 0.7706 (pm20) cc_final: 0.7438 (pm20) REVERT: A 365 PHE cc_start: 0.8064 (p90) cc_final: 0.7633 (p90) REVERT: A 379 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6783 (mm-30) REVERT: A 381 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8215 (mtmm) REVERT: A 433 MET cc_start: 0.7693 (mmm) cc_final: 0.7371 (mmm) REVERT: B 19 CYS cc_start: 0.7583 (m) cc_final: 0.7198 (m) REVERT: B 25 CYS cc_start: 0.6572 (p) cc_final: 0.6230 (p) REVERT: B 74 ASP cc_start: 0.7531 (p0) cc_final: 0.7225 (p0) REVERT: B 132 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8272 (mtm-85) REVERT: B 168 MET cc_start: 0.8116 (mmm) cc_final: 0.7869 (mmm) REVERT: B 177 LYS cc_start: 0.8380 (ttpp) cc_final: 0.8092 (ttpp) REVERT: B 181 GLU cc_start: 0.7865 (tt0) cc_final: 0.7632 (tt0) REVERT: B 216 LYS cc_start: 0.8303 (tttm) cc_final: 0.8056 (tttm) REVERT: B 230 LYS cc_start: 0.8447 (mttm) cc_final: 0.8177 (mttm) REVERT: B 266 CYS cc_start: 0.7210 (m) cc_final: 0.6774 (m) REVERT: B 305 ASP cc_start: 0.7840 (m-30) cc_final: 0.7494 (m-30) REVERT: B 324 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7762 (mt-10) REVERT: B 394 ARG cc_start: 0.7966 (mmp80) cc_final: 0.7366 (mmp80) REVERT: C 37 LYS cc_start: 0.8415 (tmtt) cc_final: 0.8108 (tmtt) REVERT: C 64 GLU cc_start: 0.6656 (pm20) cc_final: 0.6405 (pm20) outliers start: 152 outliers final: 132 residues processed: 1171 average time/residue: 0.5069 time to fit residues: 930.6824 Evaluate side-chains 1246 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1105 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 79 TYR Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 134 ASN Chi-restraints excluded: chain I residue 152 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 2 GLU Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 143 ARG Chi-restraints excluded: chain J residue 159 LEU Chi-restraints excluded: chain J residue 280 ILE Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 324 ARG Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 134 PHE Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 75 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 97 optimal weight: 8.9990 chunk 391 optimal weight: 3.9990 chunk 427 optimal weight: 0.9980 chunk 104 optimal weight: 10.0000 chunk 225 optimal weight: 0.0980 chunk 98 optimal weight: 10.0000 chunk 330 optimal weight: 9.9990 chunk 303 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 175 optimal weight: 0.4980 chunk 91 optimal weight: 0.1980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 319 GLN ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 HIS ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 1 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.155148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134948 restraints weight = 55638.113| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.72 r_work: 0.3323 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34608 Z= 0.130 Angle : 0.667 14.300 47157 Z= 0.333 Chirality : 0.047 0.258 5337 Planarity : 0.005 0.062 6017 Dihedral : 5.708 56.390 4997 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.98 % Favored : 94.00 % Rotamer: Outliers : 3.42 % Allowed : 20.36 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4280 helix: 1.60 (0.23), residues: 467 sheet: -0.41 (0.14), residues: 1288 loop : -1.19 (0.12), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 90 HIS 0.007 0.001 HIS G 52 PHE 0.024 0.002 PHE H 134 TYR 0.027 0.001 TYR F 65 ARG 0.011 0.001 ARG G 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 16) link_NAG-ASN : angle 2.18775 ( 48) hydrogen bonds : bond 0.03292 ( 1082) hydrogen bonds : angle 5.18860 ( 2859) SS BOND : bond 0.00350 ( 60) SS BOND : angle 1.67606 ( 120) covalent geometry : bond 0.00301 (34532) covalent geometry : angle 0.65920 (46989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8560 Ramachandran restraints generated. 4280 Oldfield, 0 Emsley, 4280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1243 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1117 time to evaluate : 7.147 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: D 45 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: D 104 SER cc_start: 0.7846 (m) cc_final: 0.7595 (p) REVERT: D 160 LYS cc_start: 0.8053 (tttm) cc_final: 0.7667 (mttm) REVERT: D 264 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7435 (mm-30) REVERT: D 289 ARG cc_start: 0.8087 (tpt170) cc_final: 0.7501 (tpt170) REVERT: D 319 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7197 (mm-40) REVERT: D 321 LYS cc_start: 0.8127 (mmtm) cc_final: 0.7790 (mmtm) REVERT: E 39 ASP cc_start: 0.8174 (m-30) cc_final: 0.7877 (m-30) REVERT: E 74 ASP cc_start: 0.7708 (p0) cc_final: 0.7416 (p0) REVERT: E 168 MET cc_start: 0.7589 (mmm) cc_final: 0.7167 (mmm) REVERT: E 200 GLU cc_start: 0.6994 (tt0) cc_final: 0.6648 (tt0) REVERT: E 230 LYS cc_start: 0.8293 (mttt) cc_final: 0.8028 (mttt) REVERT: E 242 ASP cc_start: 0.7037 (t70) cc_final: 0.6653 (t0) REVERT: E 303 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7158 (ttt90) REVERT: E 334 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7601 (mm-30) REVERT: E 354 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7248 (mt-10) REVERT: E 355 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7948 (mp) REVERT: F 8 MET cc_start: 0.6690 (mmm) cc_final: 0.6322 (mmm) REVERT: G 9 ASN cc_start: 0.7721 (t0) cc_final: 0.7453 (t0) REVERT: G 99 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7101 (tm-30) REVERT: G 130 LYS cc_start: 0.8422 (ttmm) cc_final: 0.8198 (ttmm) REVERT: G 234 THR cc_start: 0.8399 (p) cc_final: 0.8089 (p) REVERT: G 262 GLU cc_start: 0.7423 (mp0) cc_final: 0.6878 (mp0) REVERT: G 264 GLU cc_start: 0.7755 (mp0) cc_final: 0.7417 (mp0) REVERT: G 338 VAL cc_start: 0.8701 (p) cc_final: 0.8494 (t) REVERT: G 341 GLU cc_start: 0.8140 (mp0) cc_final: 0.7576 (mp0) REVERT: G 367 VAL cc_start: 0.8507 (t) cc_final: 0.8133 (p) REVERT: G 404 LYS cc_start: 0.8470 (tppp) cc_final: 0.7984 (tppp) REVERT: G 428 LEU cc_start: 0.8123 (mt) cc_final: 0.7546 (mt) REVERT: G 432 SER cc_start: 0.8326 (t) cc_final: 0.8121 (p) REVERT: H 60 ASP cc_start: 0.7761 (t0) cc_final: 0.7391 (t0) REVERT: H 65 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7160 (mtp180) REVERT: H 76 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8305 (mtmm) REVERT: H 78 ASP cc_start: 0.7879 (t0) cc_final: 0.7523 (t0) REVERT: H 82 LYS cc_start: 0.8139 (ptpt) cc_final: 0.7563 (ptpt) REVERT: H 151 LYS cc_start: 0.8605 (tttm) cc_final: 0.8360 (tttm) REVERT: H 168 MET cc_start: 0.7975 (mmm) cc_final: 0.6949 (mmm) REVERT: H 179 TYR cc_start: 0.8113 (m-10) cc_final: 0.7855 (m-10) REVERT: H 181 GLU cc_start: 0.6443 (mp0) cc_final: 0.5753 (mp0) REVERT: H 190 LYS cc_start: 0.7960 (tttm) cc_final: 0.7751 (mttm) REVERT: H 211 VAL cc_start: 0.7780 (m) cc_final: 0.7440 (p) REVERT: H 260 ARG cc_start: 0.8233 (ttp-110) cc_final: 0.7916 (ttp-170) REVERT: H 391 LYS cc_start: 0.7927 (tppp) cc_final: 0.7572 (tppp) REVERT: I 8 MET cc_start: 0.5020 (mmt) cc_final: 0.4745 (mmt) REVERT: J 45 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6784 (mm-30) REVERT: J 220 ARG cc_start: 0.8155 (mtt-85) cc_final: 0.7786 (mtt90) REVERT: J 234 THR cc_start: 0.8590 (t) cc_final: 0.8339 (m) REVERT: J 241 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7326 (mm-30) REVERT: J 289 ARG cc_start: 0.7635 (mmp-170) cc_final: 0.7354 (mmp-170) REVERT: J 388 ILE cc_start: 0.8734 (tp) cc_final: 0.8496 (tt) REVERT: J 408 ASN cc_start: 0.7739 (m-40) cc_final: 0.7250 (m-40) REVERT: K 3 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7934 (p) REVERT: K 20 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (ttt180) REVERT: K 33 ASN cc_start: 0.8390 (m110) cc_final: 0.8129 (m110) REVERT: K 35 TRP cc_start: 0.8745 (m-90) cc_final: 0.8175 (m-90) REVERT: K 36 ASP cc_start: 0.7709 (p0) cc_final: 0.7409 (p0) REVERT: K 60 ASP cc_start: 0.7466 (t0) cc_final: 0.6968 (t0) REVERT: K 74 ASP cc_start: 0.7440 (p0) cc_final: 0.7132 (p0) REVERT: K 81 GLU cc_start: 0.7600 (mp0) cc_final: 0.7288 (mp0) REVERT: K 138 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6356 (mt-10) REVERT: K 151 LYS cc_start: 0.8296 (ttmm) cc_final: 0.8012 (ttmm) REVERT: K 224 LYS cc_start: 0.8368 (ptmt) cc_final: 0.7901 (ptmt) REVERT: K 334 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7761 (mm-30) REVERT: L 37 LYS cc_start: 0.7727 (tmtt) cc_final: 0.7429 (tmtt) REVERT: L 62 ASP cc_start: 0.7706 (t0) cc_final: 0.7503 (t0) REVERT: L 79 TYR cc_start: 0.7577 (OUTLIER) cc_final: 0.6353 (m-80) REVERT: L 149 LYS cc_start: 0.8153 (ptpt) cc_final: 0.7932 (ptpt) REVERT: A 85 TYR cc_start: 0.8596 (t80) cc_final: 0.8366 (t80) REVERT: A 88 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7629 (mtp) REVERT: A 105 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7448 (mt-10) REVERT: A 131 VAL cc_start: 0.8583 (t) cc_final: 0.8227 (p) REVERT: A 134 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.7169 (ttp-110) REVERT: A 264 GLU cc_start: 0.7495 (pm20) cc_final: 0.7265 (pm20) REVERT: A 365 PHE cc_start: 0.8020 (p90) cc_final: 0.7569 (p90) REVERT: A 379 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6568 (mm-30) REVERT: A 381 LYS cc_start: 0.8353 (mtmm) cc_final: 0.8087 (mtmm) REVERT: A 433 MET cc_start: 0.7499 (mmm) cc_final: 0.7221 (mmm) REVERT: B 19 CYS cc_start: 0.6936 (m) cc_final: 0.6439 (m) REVERT: B 25 CYS cc_start: 0.6072 (p) cc_final: 0.5657 (p) REVERT: B 132 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.8000 (mtm-85) REVERT: B 177 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7918 (ttpp) REVERT: B 181 GLU cc_start: 0.7713 (tt0) cc_final: 0.7489 (tt0) REVERT: B 199 TYR cc_start: 0.6459 (p90) cc_final: 0.5316 (p90) REVERT: B 216 LYS cc_start: 0.8211 (tttm) cc_final: 0.7950 (tttm) REVERT: B 230 LYS cc_start: 0.8373 (mttm) cc_final: 0.8076 (mttm) REVERT: B 305 ASP cc_start: 0.7467 (m-30) cc_final: 0.7128 (m-30) REVERT: B 324 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7487 (mt-10) REVERT: B 394 ARG cc_start: 0.7755 (mmp80) cc_final: 0.7123 (mmp80) REVERT: C 16 PHE cc_start: 0.7259 (m-10) cc_final: 0.7010 (m-10) outliers start: 126 outliers final: 104 residues processed: 1165 average time/residue: 0.5327 time to fit residues: 977.6071 Evaluate side-chains 1215 residues out of total 3689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1102 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 62 CYS Chi-restraints excluded: chain D residue 102 GLN Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 301 CYS Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 GLN Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 134 PHE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain E residue 224 LYS Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 90 TRP Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 30 GLU Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 369 LEU Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 420 LEU Chi-restraints excluded: chain H residue 2 ILE Chi-restraints excluded: chain H residue 65 ARG Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 324 GLU Chi-restraints excluded: chain H residue 342 GLU Chi-restraints excluded: chain H residue 398 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 38 LEU Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 280 ILE Chi-restraints excluded: chain J residue 301 CYS Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 324 ARG Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 420 LEU Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 16 CYS Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 142 PHE Chi-restraints excluded: chain K residue 243 LEU Chi-restraints excluded: chain K residue 281 LYS Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 367 THR Chi-restraints excluded: chain K residue 371 LEU Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 79 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 143 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 223 LYS Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain B residue 3 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain P residue 48 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 93 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 309 optimal weight: 20.0000 chunk 384 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 250 optimal weight: 0.6980 chunk 348 optimal weight: 9.9990 chunk 418 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 255 optimal weight: 0.7980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 71 HIS ** E 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 408 ASN ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133714 restraints weight = 55739.822| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.67 r_work: 0.3304 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34608 Z= 0.182 Angle : 0.691 13.739 47157 Z= 0.345 Chirality : 0.048 0.369 5337 Planarity : 0.005 0.062 6017 Dihedral : 5.763 56.169 4997 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.60 % Rotamer: Outliers : 3.50 % Allowed : 20.41 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4280 helix: 1.62 (0.24), residues: 467 sheet: -0.35 (0.14), residues: 1278 loop : -1.22 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP L 90 HIS 0.007 0.001 HIS G 52 PHE 0.035 0.002 PHE B 6 TYR 0.041 0.002 TYR D 320 ARG 0.013 0.001 ARG D 134 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 16) link_NAG-ASN : angle 2.24983 ( 48) hydrogen bonds : bond 0.03440 ( 1082) hydrogen bonds : angle 5.20543 ( 2859) SS BOND : bond 0.00356 ( 60) SS BOND : angle 1.89317 ( 120) covalent geometry : bond 0.00418 (34532) covalent geometry : angle 0.68166 (46989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24771.69 seconds wall clock time: 432 minutes 24.67 seconds (25944.67 seconds total)