Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 14:48:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/04_2023/6v9q_21126_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/04_2023/6v9q_21126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/04_2023/6v9q_21126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/04_2023/6v9q_21126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/04_2023/6v9q_21126_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v9q_21126/04_2023/6v9q_21126_neut.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 60 5.49 5 S 151 5.16 5 C 17670 2.51 5 N 4836 2.21 5 O 5369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 394": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A ASP 472": "OD1" <-> "OD2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 538": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 58": "NH1" <-> "NH2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 274": "NH1" <-> "NH2" Residue "I TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ARG 286": "NH1" <-> "NH2" Residue "G PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 291": "NH1" <-> "NH2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "B PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "C PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 291": "NH1" <-> "NH2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 286": "NH1" <-> "NH2" Residue "F PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 291": "NH1" <-> "NH2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 102": "NH1" <-> "NH2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 164": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28090 Number of models: 1 Model: "" Number of chains: 13 Chain: "K" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 36} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A:plan': 1, ' A:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 3573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3573 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 8 Chain: "J" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3075 Classifications: {'peptide': 378} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 359} Chain breaks: 2 Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3050 Classifications: {'peptide': 374} Link IDs: {'PCIS': 4, 'PTRANS': 14, 'TRANS': 355} Chain breaks: 3 Chain: "G" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2453 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 15, 'TRANS': 287} Chain breaks: 2 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2731 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 17, 'TRANS': 323} Chain breaks: 1 Chain: "C" Number of atoms: 2713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2713 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 17, 'TRANS': 321} Chain breaks: 1 Chain: "D" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "E" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2704 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 17, 'TRANS': 320} Chain breaks: 1 Chain: "H" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1113 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 4 Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6062 SG CYS J 150 47.157 20.700 66.358 1.00102.18 S ATOM 6146 SG CYS J 161 42.892 16.042 84.318 1.00100.75 S ATOM 8946 SG CYS I 128 72.664 48.965 21.648 1.00 93.85 S ATOM 8967 SG CYS I 131 68.984 48.100 23.124 1.00 93.80 S ATOM 9137 SG CYS I 150 71.768 45.717 24.459 1.00 94.95 S ATOM 9221 SG CYS I 161 79.152 60.111 14.422 1.00 97.87 S ATOM 9349 SG CYS I 178 77.076 63.435 15.202 1.00 94.48 S ATOM 9370 SG CYS I 181 77.859 62.368 11.483 1.00 96.74 S Time building chain proxies: 14.80, per 1000 atoms: 0.53 Number of scatterers: 28090 At special positions: 0 Unit cell: (125.28, 201.96, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 151 16.00 P 60 15.00 O 5369 8.00 N 4836 7.00 C 17670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.16 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 150 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 131 " pdb=" ZN I 402 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 178 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 181 " pdb="ZN ZN I 402 " - pdb=" SG CYS I 161 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" ND1 HIS J 153 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 150 " pdb=" ZN J 402 " pdb="ZN ZN J 402 " - pdb=" SG CYS J 161 " 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6358 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 50 sheets defined 33.3% alpha, 15.5% beta 5 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 7.39 Creating SS restraints... Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.561A pdb=" N ALA A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 46 removed outlier: 3.735A pdb=" N LEU A 40 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.625A pdb=" N TRP A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 removed outlier: 4.533A pdb=" N THR A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.563A pdb=" N GLY A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 411 through 427 removed outlier: 3.541A pdb=" N ASN A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 512 through 519 removed outlier: 4.352A pdb=" N LYS A 517 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 519 " --> pdb=" O PHE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.717A pdb=" N ALA A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 560 removed outlier: 3.606A pdb=" N ALA A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'J' and resid 13 through 25 removed outlier: 3.839A pdb=" N ILE J 19 " --> pdb=" O GLU J 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG J 20 " --> pdb=" O SER J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 44 Processing helix chain 'J' and resid 48 through 52 removed outlier: 3.552A pdb=" N THR J 51 " --> pdb=" O GLY J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.551A pdb=" N ALA J 79 " --> pdb=" O PHE J 75 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN J 80 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 81 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.537A pdb=" N ALA J 93 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 135 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.632A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE J 144 " --> pdb=" O LEU J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.537A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.766A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 224 " --> pdb=" O ARG J 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 231 " --> pdb=" O TRP J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 246 removed outlier: 3.677A pdb=" N VAL J 241 " --> pdb=" O HIS J 237 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN J 246 " --> pdb=" O GLN J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 265 removed outlier: 3.593A pdb=" N ILE J 255 " --> pdb=" O PHE J 251 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 279 Processing helix chain 'J' and resid 297 through 307 Processing helix chain 'J' and resid 325 through 333 removed outlier: 3.615A pdb=" N THR J 329 " --> pdb=" O ALA J 325 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET J 331 " --> pdb=" O GLU J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 369 through 380 Processing helix chain 'J' and resid 386 through 390 removed outlier: 4.050A pdb=" N PHE J 389 " --> pdb=" O ASN J 386 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 390 " --> pdb=" O ARG J 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 386 through 390' Processing helix chain 'I' and resid 13 through 25 removed outlier: 3.839A pdb=" N ILE I 19 " --> pdb=" O GLU I 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG I 20 " --> pdb=" O SER I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.604A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.551A pdb=" N THR I 51 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.552A pdb=" N ALA I 79 " --> pdb=" O PHE I 75 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN I 80 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 93 removed outlier: 3.536A pdb=" N ALA I 93 " --> pdb=" O LEU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.632A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 173 Processing helix chain 'I' and resid 195 through 205 removed outlier: 3.536A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 231 removed outlier: 3.766A pdb=" N TRP I 221 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL I 224 " --> pdb=" O ARG I 220 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS I 231 " --> pdb=" O TRP I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 246 removed outlier: 3.678A pdb=" N VAL I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE I 244 " --> pdb=" O PHE I 240 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN I 246 " --> pdb=" O GLN I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 265 removed outlier: 3.594A pdb=" N ILE I 255 " --> pdb=" O PHE I 251 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 297 through 307 Processing helix chain 'I' and resid 325 through 333 removed outlier: 3.614A pdb=" N THR I 329 " --> pdb=" O ALA I 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL I 330 " --> pdb=" O LEU I 326 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET I 331 " --> pdb=" O GLU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 386 through 390 removed outlier: 4.050A pdb=" N PHE I 389 " --> pdb=" O ASN I 386 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 390 " --> pdb=" O ARG I 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 386 through 390' Processing helix chain 'G' and resid 105 through 123 Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.930A pdb=" N ASN G 135 " --> pdb=" O ARG G 131 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE G 136 " --> pdb=" O TYR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.615A pdb=" N PHE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 199 removed outlier: 3.812A pdb=" N MET G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 269 removed outlier: 3.526A pdb=" N ALA G 267 " --> pdb=" O LYS G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 312 removed outlier: 3.737A pdb=" N GLN G 311 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN G 312 " --> pdb=" O SER G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 321 removed outlier: 4.117A pdb=" N GLU G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL G 319 " --> pdb=" O HIS G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 344 removed outlier: 3.545A pdb=" N ASN G 340 " --> pdb=" O PHE G 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.558A pdb=" N VAL B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.873A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.880A pdb=" N PHE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 removed outlier: 3.781A pdb=" N MET B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE B 194 " --> pdb=" O ILE B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.576A pdb=" N ALA B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.508A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 removed outlier: 4.054A pdb=" N GLU B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 3.897A pdb=" N ASP B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N MET B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 Processing helix chain 'C' and resid 125 through 138 removed outlier: 3.837A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 138 " --> pdb=" O MET C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.857A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 199 removed outlier: 3.680A pdb=" N MET C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 194 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.554A pdb=" N ALA C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.853A pdb=" N GLN C 311 " --> pdb=" O PHE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 321 removed outlier: 3.554A pdb=" N ILE C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 319 " --> pdb=" O HIS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 removed outlier: 3.604A pdb=" N ASP C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 341 " --> pdb=" O LEU C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.890A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.782A pdb=" N PHE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 199 removed outlier: 3.620A pdb=" N MET D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 314 through 321 removed outlier: 4.017A pdb=" N GLU D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 344 removed outlier: 3.691A pdb=" N LEU D 341 " --> pdb=" O LEU D 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 123 Processing helix chain 'E' and resid 125 through 137 removed outlier: 3.906A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.829A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 199 removed outlier: 3.754A pdb=" N MET E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.529A pdb=" N ALA E 267 " --> pdb=" O LYS E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.593A pdb=" N GLN E 311 " --> pdb=" O PHE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 321 removed outlier: 4.034A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL E 319 " --> pdb=" O HIS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 344 removed outlier: 3.770A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 341 " --> pdb=" O LEU E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 removed outlier: 4.020A pdb=" N GLN F 67 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 123 Processing helix chain 'F' and resid 125 through 137 removed outlier: 3.838A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.823A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 3.935A pdb=" N MET F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.546A pdb=" N ALA F 267 " --> pdb=" O LYS F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.628A pdb=" N GLN F 311 " --> pdb=" O PHE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 321 removed outlier: 4.091A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 344 removed outlier: 3.758A pdb=" N ASP F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N MET F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN F 340 " --> pdb=" O PHE F 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 341 " --> pdb=" O LEU F 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 35 removed outlier: 4.406A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR H 33 " --> pdb=" O HIS H 29 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 80 removed outlier: 3.952A pdb=" N LEU H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 124 removed outlier: 3.502A pdb=" N ALA H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.560A pdb=" N PHE H 138 " --> pdb=" O PRO H 135 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 203 removed outlier: 4.646A pdb=" N LEU A 597 " --> pdb=" O TYR A 543 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 203 removed outlier: 7.206A pdb=" N ILE A 590 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU A 572 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLU A 592 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR A 570 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 594 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 16.048A pdb=" N SER A 566 " --> pdb=" O PRO A 627 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 568 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 236 through 237 removed outlier: 5.973A pdb=" N LEU A 261 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 443 removed outlier: 4.013A pdb=" N SER A 437 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'A' and resid 447 through 448 Processing sheet with id=AB1, first strand: chain 'J' and resid 95 through 100 removed outlier: 3.669A pdb=" N THR J 97 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA J 107 " --> pdb=" O THR J 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 322 through 323 removed outlier: 3.511A pdb=" N PHE J 367 " --> pdb=" O MET J 323 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 95 through 100 removed outlier: 3.669A pdb=" N THR I 97 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA I 107 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.511A pdb=" N PHE I 367 " --> pdb=" O MET I 323 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 102 through 103 Processing sheet with id=AB6, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.506A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 18 through 24 current: chain 'G' and resid 151 through 158 removed outlier: 6.448A pdb=" N TRP G 152 " --> pdb=" O ASP G 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP G 170 " --> pdb=" O TRP G 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 28 through 31 removed outlier: 3.727A pdb=" N ARG G 28 " --> pdb=" O TRP G 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 84 through 93 current: chain 'G' and resid 248 through 251 Processing sheet with id=AB8, first strand: chain 'G' and resid 270 through 272 Processing sheet with id=AB9, first strand: chain 'G' and resid 289 through 290 removed outlier: 3.717A pdb=" N THR G 295 " --> pdb=" O HIS G 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AC2, first strand: chain 'B' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 18 through 23 current: chain 'B' and resid 151 through 155 removed outlier: 6.559A pdb=" N TRP B 152 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 170 " --> pdb=" O TRP B 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 84 through 93 current: chain 'B' and resid 248 through 251 Processing sheet with id=AC4, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AC5, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'B' and resid 289 through 290 removed outlier: 3.718A pdb=" N THR B 295 " --> pdb=" O HIS B 290 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 102 through 103 Processing sheet with id=AC8, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.802A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP C 152 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 170 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.110A pdb=" N PHE C 20 " --> pdb=" O PRO C 257 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL C 22 " --> pdb=" O ARG C 255 " (cutoff:3.500A) removed outlier: 14.136A pdb=" N ARG C 255 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 35 through 41 removed outlier: 8.473A pdb=" N SER C 243 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN C 72 " --> pdb=" O SER C 243 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AD3, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.718A pdb=" N THR C 295 " --> pdb=" O HIS C 290 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 102 through 103 Processing sheet with id=AD5, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.941A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP D 152 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 170 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.114A pdb=" N PHE D 20 " --> pdb=" O PRO D 257 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N VAL D 22 " --> pdb=" O ARG D 255 " (cutoff:3.500A) removed outlier: 14.029A pdb=" N ARG D 255 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 35 through 41 Processing sheet with id=AD8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AD9, first strand: chain 'D' and resid 289 through 290 removed outlier: 3.612A pdb=" N THR D 295 " --> pdb=" O HIS D 290 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 102 through 103 Processing sheet with id=AE2, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.502A pdb=" N HIS E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 152 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP E 170 " --> pdb=" O TRP E 152 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 29 through 31 removed outlier: 4.187A pdb=" N PHE E 20 " --> pdb=" O PRO E 257 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N VAL E 22 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 14.005A pdb=" N ARG E 255 " --> pdb=" O VAL E 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 35 through 41 Processing sheet with id=AE5, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AE6, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.665A pdb=" N THR E 295 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 102 through 103 Processing sheet with id=AE8, first strand: chain 'F' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 23 current: chain 'F' and resid 151 through 158 removed outlier: 6.557A pdb=" N TRP F 152 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP F 170 " --> pdb=" O TRP F 152 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 29 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 84 through 93 current: chain 'F' and resid 248 through 251 Processing sheet with id=AF1, first strand: chain 'F' and resid 35 through 38 Processing sheet with id=AF2, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AF3, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AF4, first strand: chain 'H' and resid 7 through 9 Processing sheet with id=AF5, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.666A pdb=" N ARG H 102 " --> pdb=" O ARG H 168 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2409 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 12.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6795 1.33 - 1.45: 6552 1.45 - 1.57: 15234 1.57 - 1.69: 120 1.69 - 1.81: 219 Bond restraints: 28920 Sorted by residual: bond pdb=" N GLU G 280 " pdb=" CA GLU G 280 " ideal model delta sigma weight residual 1.453 1.489 -0.036 9.20e-03 1.18e+04 1.50e+01 bond pdb=" N VAL J 268 " pdb=" CA VAL J 268 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.11e-02 8.12e+03 1.25e+01 bond pdb=" N VAL H 42 " pdb=" CA VAL H 42 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 bond pdb=" N GLU G 277 " pdb=" CA GLU G 277 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" N ASP G 273 " pdb=" CA ASP G 273 " ideal model delta sigma weight residual 1.458 1.487 -0.029 9.00e-03 1.23e+04 1.03e+01 ... (remaining 28915 not shown) Histogram of bond angle deviations from ideal: 94.93 - 103.01: 296 103.01 - 111.08: 11191 111.08 - 119.16: 12850 119.16 - 127.23: 14668 127.23 - 135.31: 500 Bond angle restraints: 39505 Sorted by residual: angle pdb=" N ALA E 205 " pdb=" CA ALA E 205 " pdb=" C ALA E 205 " ideal model delta sigma weight residual 111.02 118.93 -7.91 1.25e+00 6.40e-01 4.00e+01 angle pdb=" N ALA C 205 " pdb=" CA ALA C 205 " pdb=" C ALA C 205 " ideal model delta sigma weight residual 111.02 118.66 -7.64 1.25e+00 6.40e-01 3.74e+01 angle pdb=" N ALA F 205 " pdb=" CA ALA F 205 " pdb=" C ALA F 205 " ideal model delta sigma weight residual 111.02 118.33 -7.31 1.25e+00 6.40e-01 3.42e+01 angle pdb=" C GLU C 96 " pdb=" N LEU C 97 " pdb=" CA LEU C 97 " ideal model delta sigma weight residual 120.29 128.36 -8.07 1.42e+00 4.96e-01 3.23e+01 angle pdb=" N MET A 564 " pdb=" CA MET A 564 " pdb=" C MET A 564 " ideal model delta sigma weight residual 110.91 117.55 -6.64 1.17e+00 7.31e-01 3.22e+01 ... (remaining 39500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 16791 34.87 - 69.74: 239 69.74 - 104.60: 20 104.60 - 139.47: 1 139.47 - 174.34: 5 Dihedral angle restraints: 17056 sinusoidal: 7279 harmonic: 9777 Sorted by residual: dihedral pdb=" O4' U K 42 " pdb=" C1' U K 42 " pdb=" N1 U K 42 " pdb=" C2 U K 42 " ideal model delta sinusoidal sigma weight residual 200.00 44.90 155.10 1 1.50e+01 4.44e-03 8.14e+01 dihedral pdb=" O4' C K 38 " pdb=" C1' C K 38 " pdb=" N1 C K 38 " pdb=" C2 C K 38 " ideal model delta sinusoidal sigma weight residual 232.00 57.66 174.34 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C K 12 " pdb=" C1' C K 12 " pdb=" N1 C K 12 " pdb=" C2 C K 12 " ideal model delta sinusoidal sigma weight residual 200.00 76.85 123.15 1 1.50e+01 4.44e-03 6.60e+01 ... (remaining 17053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3521 0.079 - 0.159: 727 0.159 - 0.238: 97 0.238 - 0.318: 26 0.318 - 0.397: 3 Chirality restraints: 4374 Sorted by residual: chirality pdb=" CG LEU G 112 " pdb=" CB LEU G 112 " pdb=" CD1 LEU G 112 " pdb=" CD2 LEU G 112 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB THR D 146 " pdb=" CA THR D 146 " pdb=" OG1 THR D 146 " pdb=" CG2 THR D 146 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C3' C K 46 " pdb=" C4' C K 46 " pdb=" O3' C K 46 " pdb=" C2' C K 46 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 4371 not shown) Planarity restraints: 4822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 11 " -0.055 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO H 12 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 9 " 0.018 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR D 9 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR D 9 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR D 9 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 9 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 9 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 9 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 9 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 194 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.49e+00 pdb=" N PRO A 195 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " -0.043 5.00e-02 4.00e+02 ... (remaining 4819 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 283 2.61 - 3.18: 22430 3.18 - 3.76: 42349 3.76 - 4.33: 61001 4.33 - 4.90: 100201 Nonbonded interactions: 226264 Sorted by model distance: nonbonded pdb=" O2' A K 44 " pdb=" O5' A K 45 " model vdw 2.040 2.440 nonbonded pdb=" O2' A K 44 " pdb=" OP1 A K 45 " model vdw 2.102 2.440 nonbonded pdb=" O SER G 95 " pdb=" OG SER G 95 " model vdw 2.132 2.440 nonbonded pdb=" O SER F 95 " pdb=" OG SER F 95 " model vdw 2.134 2.440 nonbonded pdb=" O SER D 95 " pdb=" OG SER D 95 " model vdw 2.149 2.440 ... (remaining 226259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'C' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'D' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'E' and (resid 1 through 36 or resid 73 through 350)) selection = (chain 'F' and (resid 1 through 36 or resid 73 through 228 or resid 242 through \ 350)) selection = (chain 'G' and (resid 1 through 228 or resid 242 through 350)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 265 or resid 270 through 391 or resid 401 throug \ h 402)) } 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.020 Extract box with map and model: 7.650 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 78.840 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.120 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:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.008 0.110 28920 Z= 0.544 Angle : 1.123 11.907 39505 Z= 0.660 Chirality : 0.068 0.397 4374 Planarity : 0.008 0.083 4822 Dihedral : 12.820 174.339 10698 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.97 % 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: -4.27 (0.11), residues: 3269 helix: -3.89 (0.09), residues: 1090 sheet: -1.51 (0.22), residues: 497 loop : -2.47 (0.12), residues: 1682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 745 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 12 residues processed: 778 average time/residue: 1.5710 time to fit residues: 1400.8214 Evaluate side-chains 374 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 362 time to evaluate : 3.602 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.2484 time to fit residues: 5.2676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 282 optimal weight: 1.9990 chunk 253 optimal weight: 0.0570 chunk 140 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 0.0370 chunk 194 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN A 226 HIS A 227 GLN A 235 HIS A 420 HIS A 486 ASN A 610 ASN J 60 ASN J 66 ASN J 143 HIS J 237 HIS J 313 GLN J 381 GLN I 47 ASN I 60 ASN I 66 ASN ** I 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 237 HIS I 296 HIS I 324 ASN G 299 HIS G 315 HIS G 328 GLN B 42 GLN B 77 HIS B 84 HIS B 110 GLN B 114 GLN B 299 HIS B 348 GLN C 77 HIS C 110 GLN C 184 ASN C 241 GLN C 299 HIS C 315 HIS D 77 HIS D 84 HIS D 110 GLN D 214 HIS D 299 HIS E 42 GLN E 55 GLN E 77 HIS E 299 HIS F 99 GLN F 299 HIS F 328 GLN H 16 ASN H 32 ASN H 39 ASN ** H 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 150 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 28920 Z= 0.199 Angle : 0.636 10.435 39505 Z= 0.329 Chirality : 0.043 0.235 4374 Planarity : 0.006 0.066 4822 Dihedral : 11.730 178.747 4306 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 4.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -2.89 (0.13), residues: 3269 helix: -2.08 (0.12), residues: 1106 sheet: -0.91 (0.24), residues: 472 loop : -2.07 (0.13), residues: 1691 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 419 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 48 residues processed: 512 average time/residue: 1.3466 time to fit residues: 808.1903 Evaluate side-chains 370 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 322 time to evaluate : 3.201 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 39 residues processed: 10 average time/residue: 0.8371 time to fit residues: 15.0514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 168 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 chunk 328 optimal weight: 7.9990 chunk 270 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 HIS J 313 GLN J 381 GLN I 42 GLN I 50 GLN I 80 GLN G 35 ASN G 77 HIS B 114 GLN C 241 GLN D 110 GLN E 55 GLN F 99 GLN H 71 GLN ** H 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 28920 Z= 0.255 Angle : 0.630 10.017 39505 Z= 0.323 Chirality : 0.044 0.291 4374 Planarity : 0.005 0.064 4822 Dihedral : 11.593 178.288 4306 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.94 (0.13), residues: 3269 helix: -0.89 (0.14), residues: 1110 sheet: -0.69 (0.23), residues: 499 loop : -1.73 (0.14), residues: 1660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 343 time to evaluate : 3.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 72 residues processed: 467 average time/residue: 1.3418 time to fit residues: 741.1454 Evaluate side-chains 373 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 301 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 60 residues processed: 14 average time/residue: 0.6237 time to fit residues: 16.5960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 300 optimal weight: 0.0570 chunk 228 optimal weight: 5.9990 chunk 157 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 304 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 ASN J 345 GLN I 50 GLN I 80 GLN G 35 ASN B 114 GLN C 110 GLN C 349 HIS D 110 GLN E 55 GLN H 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 28920 Z= 0.232 Angle : 0.592 9.407 39505 Z= 0.304 Chirality : 0.042 0.218 4374 Planarity : 0.005 0.064 4822 Dihedral : 11.415 179.635 4306 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.45 (0.14), residues: 3269 helix: -0.31 (0.15), residues: 1126 sheet: -0.38 (0.24), residues: 486 loop : -1.59 (0.14), residues: 1657 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 317 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 77 residues processed: 429 average time/residue: 1.3271 time to fit residues: 670.4370 Evaluate side-chains 365 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 288 time to evaluate : 3.180 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 64 residues processed: 15 average time/residue: 0.6430 time to fit residues: 17.1778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 268 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 240 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 275 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 164 optimal weight: 0.0470 chunk 289 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN J 60 ASN J 313 GLN I 50 GLN I 80 GLN G 35 ASN B 184 ASN C 110 GLN D 110 GLN E 55 GLN H 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 28920 Z= 0.179 Angle : 0.550 9.161 39505 Z= 0.283 Chirality : 0.041 0.209 4374 Planarity : 0.005 0.054 4822 Dihedral : 11.205 177.716 4306 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -1.07 (0.14), residues: 3269 helix: 0.16 (0.16), residues: 1121 sheet: -0.18 (0.24), residues: 476 loop : -1.49 (0.14), residues: 1672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 313 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 80 residues processed: 413 average time/residue: 1.3043 time to fit residues: 638.7595 Evaluate side-chains 373 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 293 time to evaluate : 3.323 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 71 residues processed: 10 average time/residue: 0.5354 time to fit residues: 12.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 63 optimal weight: 30.0000 chunk 189 optimal weight: 0.0980 chunk 79 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 268 optimal weight: 0.5980 chunk 149 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 169 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 23 ASN J 345 GLN I 50 GLN I 80 GLN I 345 GLN G 35 ASN B 110 GLN B 114 GLN B 184 ASN C 110 GLN D 110 GLN E 55 GLN H 32 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 28920 Z= 0.196 Angle : 0.560 9.278 39505 Z= 0.285 Chirality : 0.041 0.199 4374 Planarity : 0.005 0.053 4822 Dihedral : 11.120 177.467 4306 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.17 % Favored : 94.80 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.80 (0.14), residues: 3269 helix: 0.49 (0.16), residues: 1110 sheet: -0.03 (0.24), residues: 483 loop : -1.40 (0.14), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 305 time to evaluate : 3.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 81 residues processed: 402 average time/residue: 1.3185 time to fit residues: 627.1209 Evaluate side-chains 373 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 292 time to evaluate : 3.330 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 69 residues processed: 13 average time/residue: 0.5333 time to fit residues: 14.3458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 311 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 235 optimal weight: 0.6980 chunk 182 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 321 optimal weight: 6.9990 chunk 201 optimal weight: 0.0970 chunk 196 optimal weight: 0.8980 chunk 148 optimal weight: 0.0870 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 237 HIS I 50 GLN I 80 GLN G 35 ASN B 114 GLN B 184 ASN B 348 GLN C 110 GLN D 110 GLN E 55 GLN H 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 28920 Z= 0.143 Angle : 0.527 10.730 39505 Z= 0.268 Chirality : 0.039 0.218 4374 Planarity : 0.004 0.064 4822 Dihedral : 10.939 175.773 4306 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.54 (0.15), residues: 3269 helix: 0.78 (0.16), residues: 1109 sheet: 0.10 (0.24), residues: 484 loop : -1.31 (0.14), residues: 1676 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 307 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 78 residues processed: 398 average time/residue: 1.3351 time to fit residues: 630.2607 Evaluate side-chains 363 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 285 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 69 residues processed: 10 average time/residue: 0.5268 time to fit residues: 12.1296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 199 optimal weight: 0.0980 chunk 128 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 62 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 253 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 345 GLN I 50 GLN I 80 GLN G 35 ASN B 110 GLN B 114 GLN C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 28920 Z= 0.137 Angle : 0.515 11.909 39505 Z= 0.262 Chirality : 0.039 0.200 4374 Planarity : 0.004 0.060 4822 Dihedral : 10.789 175.158 4306 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.32 % Favored : 94.65 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.36 (0.15), residues: 3269 helix: 0.97 (0.16), residues: 1112 sheet: 0.19 (0.24), residues: 474 loop : -1.21 (0.15), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 307 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 75 residues processed: 389 average time/residue: 1.3137 time to fit residues: 605.3002 Evaluate side-chains 369 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 294 time to evaluate : 3.295 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 68 residues processed: 9 average time/residue: 0.4557 time to fit residues: 10.7321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 292 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 281 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 271 optimal weight: 0.5980 chunk 283 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 GLN A 599 ASN J 345 GLN I 50 GLN I 66 ASN I 80 GLN G 35 ASN B 114 GLN B 348 GLN C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 28920 Z= 0.170 Angle : 0.543 10.689 39505 Z= 0.275 Chirality : 0.040 0.214 4374 Planarity : 0.004 0.067 4822 Dihedral : 10.783 176.049 4306 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.27 (0.15), residues: 3269 helix: 1.06 (0.16), residues: 1108 sheet: 0.22 (0.24), residues: 484 loop : -1.16 (0.15), residues: 1677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 294 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 82 residues processed: 378 average time/residue: 1.3527 time to fit residues: 606.7792 Evaluate side-chains 356 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 274 time to evaluate : 3.306 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 73 residues processed: 11 average time/residue: 0.7704 time to fit residues: 15.8936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 196 optimal weight: 0.8980 chunk 317 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 306 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 204 optimal weight: 2.9990 chunk 162 optimal weight: 0.0870 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 345 GLN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 80 GLN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN I 345 GLN G 35 ASN C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 28920 Z= 0.154 Angle : 0.538 13.617 39505 Z= 0.271 Chirality : 0.039 0.188 4374 Planarity : 0.004 0.066 4822 Dihedral : 10.700 175.493 4306 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.55 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.19 (0.15), residues: 3269 helix: 1.16 (0.16), residues: 1102 sheet: 0.28 (0.25), residues: 472 loop : -1.14 (0.15), residues: 1695 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 288 time to evaluate : 3.292 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 76 residues processed: 364 average time/residue: 1.2874 time to fit residues: 556.2646 Evaluate side-chains 354 residues out of total 2956 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 278 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 73 residues processed: 4 average time/residue: 0.6835 time to fit residues: 8.1587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 334 random chunks: chunk 210 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 39 optimal weight: 0.0570 chunk 73 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN J 345 GLN ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN I 80 GLN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN I 345 GLN G 35 ASN G 84 HIS C 84 HIS C 110 GLN D 110 GLN E 55 GLN ** E 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS H 32 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.156503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.104423 restraints weight = 33432.819| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.86 r_work: 0.2882 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 28920 Z= 0.374 Angle : 0.686 12.821 39505 Z= 0.348 Chirality : 0.046 0.219 4374 Planarity : 0.005 0.067 4822 Dihedral : 11.299 177.961 4306 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.79 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.97 % 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: -0.56 (0.15), residues: 3269 helix: 0.75 (0.16), residues: 1108 sheet: 0.19 (0.25), residues: 476 loop : -1.34 (0.14), residues: 1685 =============================================================================== Job complete usr+sys time: 10950.84 seconds wall clock time: 195 minutes 20.93 seconds (11720.93 seconds total)