Starting phenix.real_space_refine (version: dev) on Wed Dec 21 06:01:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1m_14448/12_2022/7z1m_14448_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1m_14448/12_2022/7z1m_14448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1m_14448/12_2022/7z1m_14448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1m_14448/12_2022/7z1m_14448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1m_14448/12_2022/7z1m_14448_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1m_14448/12_2022/7z1m_14448_updated.pdb" } resolution = 3.4 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= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "D TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 22": "OD1" <-> "OD2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 159": "OD1" <-> "OD2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F ASP 140": "OD1" <-> "OD2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 145": "OD1" <-> "OD2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "I TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K ASP 85": "OD1" <-> "OD2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "M PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 259": "OD1" <-> "OD2" Residue "P TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 27": "OD1" <-> "OD2" Residue "Q TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 42122 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11231 Classifications: {'peptide': 1436} Link IDs: {'PTRANS': 66, 'TRANS': 1369} Chain breaks: 2 Chain: "B" Number of atoms: 8693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8693 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 41, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "D" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1185 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1610 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1083 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 872 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 1 Chain: "N" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1171 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain breaks: 2 Chain: "O" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4577 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} Chain breaks: 1 Chain: "P" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1162 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "Q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 172 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna3p': 7} Chain: "S" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "T" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 578 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 1} Classifications: {'undetermined': 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} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 500 SG CYS A 67 113.988 78.063 107.654 1.00103.78 S ATOM 518 SG CYS A 70 112.881 74.451 107.042 1.00 98.55 S ATOM 565 SG CYS A 77 111.227 77.398 105.146 1.00 94.29 S ATOM 803 SG CYS A 107 82.546 99.044 137.789 1.00 94.17 S ATOM 826 SG CYS A 110 83.424 96.005 139.954 1.00 94.94 S ATOM 1192 SG CYS A 154 79.865 97.074 139.637 1.00104.66 S ATOM 1216 SG CYS A 157 82.310 99.093 141.702 1.00103.18 S ATOM 19497 SG CYS B1095 99.467 69.121 117.110 1.00 88.46 S ATOM 19520 SG CYS B1098 98.875 72.818 117.497 1.00 85.02 S ATOM 19586 SG CYS B1107 102.372 71.632 116.924 1.00 91.15 S ATOM 19606 SG CYS B1110 100.775 70.817 120.233 1.00 95.02 S ATOM 28918 SG CYS I 5 61.534 152.241 107.302 1.00148.90 S ATOM 28937 SG CYS I 8 65.165 151.369 107.468 1.00149.54 S ATOM 29065 SG CYS I 26 63.010 149.978 110.253 1.00150.50 S ATOM 29088 SG CYS I 29 63.701 153.655 110.055 1.00157.64 S ATOM 29463 SG CYS I 75 13.698 124.762 98.587 1.00246.69 S ATOM 29665 SG CYS I 100 14.919 122.695 96.536 1.00237.06 S ATOM 29686 SG CYS I 103 17.084 124.999 98.348 1.00240.25 S ATOM 29805 SG CYS J 7 93.837 90.248 38.579 1.00 83.27 S ATOM 29828 SG CYS J 10 93.351 87.552 35.887 1.00 81.74 S ATOM 30108 SG CYS J 45 90.573 90.010 36.850 1.00 85.95 S ATOM 30114 SG CYS J 46 93.665 90.897 34.690 1.00 84.92 S ATOM 31171 SG CYS L 31 127.397 109.298 58.754 1.00104.55 S ATOM 31191 SG CYS L 34 129.239 110.075 55.649 1.00106.37 S ATOM 31295 SG CYS L 48 131.281 109.469 58.626 1.00112.53 S ATOM 31318 SG CYS L 51 129.227 112.670 58.528 1.00113.33 S Time building chain proxies: 23.14, per 1000 atoms: 0.55 Number of scatterers: 42122 At special positions: 0 Unit cell: (148.863, 193.626, 197.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 218 16.00 P 53 15.00 Mg 1 11.99 O 8047 8.00 N 7263 7.00 C 26533 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.68 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 33 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 50 sheets defined 35.4% alpha, 12.6% beta 16 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 15.79 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 284 through 305 Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 353 through 357 Processing helix chain 'A' and resid 363 through 366 No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.255A pdb=" N THR A 506 " --> pdb=" O CYS A 503 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 558 through 564 Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.646A pdb=" N SER A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 677 through 704 Proline residue: A 687 - end of helix removed outlier: 3.968A pdb=" N ALA A 690 " --> pdb=" O GLY A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 716 No H-bonds generated for 'chain 'A' and resid 714 through 716' Processing helix chain 'A' and resid 723 through 747 removed outlier: 3.723A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 842 through 845 No H-bonds generated for 'chain 'A' and resid 842 through 845' Processing helix chain 'A' and resid 858 through 892 removed outlier: 4.420A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 956 through 972 Proline residue: A 969 - end of helix Processing helix chain 'A' and resid 999 through 1026 removed outlier: 3.970A pdb=" N LEU A1022 " --> pdb=" O ALA A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1059 Processing helix chain 'A' and resid 1064 through 1080 Processing helix chain 'A' and resid 1089 through 1103 Proline residue: A1100 - end of helix removed outlier: 3.957A pdb=" N GLN A1103 " --> pdb=" O GLU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1130 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.596A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1168 No H-bonds generated for 'chain 'A' and resid 1166 through 1168' Processing helix chain 'A' and resid 1190 through 1196 Processing helix chain 'A' and resid 1202 through 1210 Processing helix chain 'A' and resid 1255 through 1269 Proline residue: A1268 - end of helix Processing helix chain 'A' and resid 1300 through 1305 Processing helix chain 'A' and resid 1319 through 1345 removed outlier: 8.070A pdb=" N ILE A1328 " --> pdb=" O SER A1324 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N GLU A1329 " --> pdb=" O VAL A1325 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A1330 " --> pdb=" O LEU A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 Processing helix chain 'A' and resid 1373 through 1379 removed outlier: 3.689A pdb=" N SER A1377 " --> pdb=" O ARG A1373 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A1378 " --> pdb=" O PHE A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1389 Processing helix chain 'A' and resid 1392 through 1402 Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1424 through 1426 No H-bonds generated for 'chain 'A' and resid 1424 through 1426' Processing helix chain 'A' and resid 1438 through 1440 No H-bonds generated for 'chain 'A' and resid 1438 through 1440' Processing helix chain 'A' and resid 1447 through 1451 Processing helix chain 'B' and resid 41 through 54 removed outlier: 4.554A pdb=" N TRP B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS B 46 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Proline residue: B 49 - end of helix removed outlier: 4.242A pdb=" N VAL B 54 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 79 removed outlier: 3.786A pdb=" N SER B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU B 73 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LYS B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 121 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 277 through 292 removed outlier: 5.243A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 380 through 407 Processing helix chain 'B' and resid 418 through 421 Processing helix chain 'B' and resid 423 through 439 removed outlier: 4.282A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 527 through 536 Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 651 through 656 removed outlier: 3.805A pdb=" N ASP B 656 " --> pdb=" O ASN B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'B' and resid 696 through 708 removed outlier: 4.548A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 764 through 766 No H-bonds generated for 'chain 'B' and resid 764 through 766' Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 946 through 952 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 970 Processing helix chain 'B' and resid 984 through 994 Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1054 through 1056 No H-bonds generated for 'chain 'B' and resid 1054 through 1056' Processing helix chain 'B' and resid 1064 through 1073 Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1123 through 1134 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.809A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 241 through 250 Processing helix chain 'C' and resid 278 through 280 No H-bonds generated for 'chain 'C' and resid 278 through 280' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 310 through 330 Processing helix chain 'D' and resid 13 through 27 Processing helix chain 'D' and resid 31 through 37 Processing helix chain 'D' and resid 53 through 67 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'E' and resid 2 through 25 removed outlier: 4.191A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASN E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 102 Processing helix chain 'E' and resid 118 through 123 removed outlier: 4.500A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 117 through 127 removed outlier: 3.762A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 32 through 38 removed outlier: 4.109A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.805A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.897A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 4.539A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 141 Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 184 through 199 Processing helix chain 'M' and resid 230 through 239 Processing helix chain 'M' and resid 252 through 264 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'N' and resid 214 through 223 removed outlier: 4.042A pdb=" N ARG N 217 " --> pdb=" O THR N 214 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA N 222 " --> pdb=" O ILE N 219 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU N 223 " --> pdb=" O GLN N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 296 Processing helix chain 'O' and resid 28 through 34 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 76 through 82 Processing helix chain 'O' and resid 88 through 100 Processing helix chain 'O' and resid 124 through 131 Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 150 through 166 Processing helix chain 'O' and resid 171 through 177 removed outlier: 3.871A pdb=" N SER O 177 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 197 Processing helix chain 'O' and resid 205 through 208 Processing helix chain 'O' and resid 211 through 224 Processing helix chain 'O' and resid 234 through 258 removed outlier: 3.650A pdb=" N ASN O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS O 255 " --> pdb=" O LYS O 251 " (cutoff:3.500A) Proline residue: O 256 - end of helix Processing helix chain 'O' and resid 284 through 302 removed outlier: 3.884A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 318 Processing helix chain 'O' and resid 329 through 333 Processing helix chain 'O' and resid 335 through 337 No H-bonds generated for 'chain 'O' and resid 335 through 337' Processing helix chain 'O' and resid 339 through 355 removed outlier: 3.642A pdb=" N GLU O 353 " --> pdb=" O ALA O 349 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 369 removed outlier: 4.012A pdb=" N ARG O 368 " --> pdb=" O ASP O 365 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS O 369 " --> pdb=" O LEU O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 461 Processing helix chain 'O' and resid 480 through 513 Proline residue: O 485 - end of helix Proline residue: O 502 - end of helix removed outlier: 3.670A pdb=" N MET O 505 " --> pdb=" O GLY O 501 " (cutoff:3.500A) Processing helix chain 'O' and resid 519 through 525 Processing helix chain 'O' and resid 530 through 543 removed outlier: 4.224A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR O 543 " --> pdb=" O SER O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 559 through 561 No H-bonds generated for 'chain 'O' and resid 559 through 561' Processing helix chain 'O' and resid 570 through 598 Processing helix chain 'O' and resid 600 through 606 Processing helix chain 'O' and resid 615 through 618 No H-bonds generated for 'chain 'O' and resid 615 through 618' Processing helix chain 'O' and resid 621 through 648 Processing helix chain 'P' and resid 172 through 190 Processing helix chain 'P' and resid 194 through 196 No H-bonds generated for 'chain 'P' and resid 194 through 196' Processing helix chain 'P' and resid 218 through 227 Processing helix chain 'P' and resid 237 through 249 Processing helix chain 'P' and resid 265 through 270 Processing helix chain 'Q' and resid 49 through 66 Processing helix chain 'Q' and resid 129 through 131 No H-bonds generated for 'chain 'Q' and resid 129 through 131' Processing helix chain 'Q' and resid 134 through 136 No H-bonds generated for 'chain 'Q' and resid 134 through 136' Processing sheet with id= A, first strand: chain 'A' and resid 15 through 17 Processing sheet with id= B, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 166 Processing sheet with id= D, first strand: chain 'A' and resid 376 through 380 Processing sheet with id= E, first strand: chain 'A' and resid 381 through 383 removed outlier: 6.146A pdb=" N PHE A 498 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.941A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 626 through 629 removed outlier: 3.675A pdb=" N ILE A 653 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 661 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG A 655 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1140 through 1144 Processing sheet with id= I, first strand: chain 'A' and resid 1222 through 1225 removed outlier: 4.209A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 Processing sheet with id= K, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= L, first strand: chain 'B' and resid 133 through 137 Processing sheet with id= M, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= N, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= O, first strand: chain 'B' and resid 205 through 210 removed outlier: 4.770A pdb=" N VAL B 216 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 442 through 444 Processing sheet with id= Q, first strand: chain 'B' and resid 472 through 474 Processing sheet with id= R, first strand: chain 'B' and resid 538 through 540 removed outlier: 6.680A pdb=" N VAL B 555 " --> pdb=" O ILE B 562 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 609 through 613 Processing sheet with id= T, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.930A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 753 through 759 removed outlier: 4.167A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 846 through 848 Processing sheet with id= W, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id= X, first strand: chain 'B' and resid 771 through 774 removed outlier: 7.618A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.390A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 41 through 47 removed outlier: 7.013A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE C 54 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.248A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 256 through 259 removed outlier: 3.659A pdb=" N GLU C 264 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 161 through 163 Processing sheet with id= AD, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.694A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 152 through 156 removed outlier: 3.915A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 133 through 135 Processing sheet with id= AG, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.880A pdb=" N THR G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N PHE G 77 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N CYS G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.599A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SER G 100 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE G 89 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU G 197 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU G 153 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA G 195 " --> pdb=" O GLU G 153 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AJ, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.792A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.175A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE H 6 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 13 through 15 Processing sheet with id= AM, first strand: chain 'I' and resid 64 through 66 Processing sheet with id= AN, first strand: chain 'K' and resid 47 through 49 Processing sheet with id= AO, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AP, first strand: chain 'M' and resid 109 through 112 removed outlier: 3.703A pdb=" N ALA M 109 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'M' and resid 152 through 154 removed outlier: 7.645A pdb=" N LEU M 85 " --> pdb=" O GLU M 174 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL M 176 " --> pdb=" O LEU M 85 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL M 87 " --> pdb=" O VAL M 176 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN M 178 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN M 89 " --> pdb=" O GLN M 178 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 159 through 164 Processing sheet with id= AS, first strand: chain 'N' and resid 306 through 308 removed outlier: 4.666A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'N' and resid 393 through 398 removed outlier: 6.821A pdb=" N ALA N 396 " --> pdb=" O LEU N 408 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU N 408 " --> pdb=" O ALA N 396 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N SER N 398 " --> pdb=" O ALA N 406 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ALA N 406 " --> pdb=" O SER N 398 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'O' and resid 106 through 110 Processing sheet with id= AV, first strand: chain 'O' and resid 168 through 170 Processing sheet with id= AW, first strand: chain 'O' and resid 547 through 552 Processing sheet with id= AX, first strand: chain 'P' and resid 253 through 257 removed outlier: 3.936A pdb=" N VAL P 256 " --> pdb=" O CYS P 260 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) 1432 hydrogen bonds defined for protein. 4086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 21.24 Time building geometry restraints manager: 19.19 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: 13451 1.34 - 1.46: 8168 1.46 - 1.58: 20913 1.58 - 1.70: 111 1.70 - 1.82: 354 Bond restraints: 42997 Sorted by residual: bond pdb=" C15 4QM A2003 " pdb=" C16 4QM A2003 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C15 4QM C 401 " pdb=" C16 4QM C 401 " ideal model delta sigma weight residual 1.529 1.592 -0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" C19 4QM C 401 " pdb=" C2 4QM C 401 " ideal model delta sigma weight residual 1.551 1.612 -0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" C16 4QM C 401 " pdb=" C17 4QM C 401 " ideal model delta sigma weight residual 1.527 1.586 -0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" C16 4QM A2003 " pdb=" C17 4QM A2003 " ideal model delta sigma weight residual 1.527 1.585 -0.058 2.00e-02 2.50e+03 8.54e+00 ... (remaining 42992 not shown) Histogram of bond angle deviations from ideal: 94.14 - 102.62: 246 102.62 - 111.10: 16764 111.10 - 119.58: 20491 119.58 - 128.06: 20481 128.06 - 136.54: 315 Bond angle restraints: 58297 Sorted by residual: angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 113.71 107.60 6.11 9.50e-01 1.11e+00 4.13e+01 angle pdb=" N PRO E 128 " pdb=" CA PRO E 128 " pdb=" C PRO E 128 " ideal model delta sigma weight residual 110.70 117.05 -6.35 1.22e+00 6.72e-01 2.71e+01 angle pdb=" CA PRO E 128 " pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 117.93 123.98 -6.05 1.20e+00 6.94e-01 2.55e+01 angle pdb=" N GLU D 155 " pdb=" CA GLU D 155 " pdb=" CB GLU D 155 " ideal model delta sigma weight residual 110.30 117.66 -7.36 1.54e+00 4.22e-01 2.28e+01 angle pdb=" CA ARG O 145 " pdb=" CB ARG O 145 " pdb=" CG ARG O 145 " ideal model delta sigma weight residual 114.10 123.34 -9.24 2.00e+00 2.50e-01 2.13e+01 ... (remaining 58292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.29: 24826 27.29 - 54.57: 1179 54.57 - 81.86: 133 81.86 - 109.15: 25 109.15 - 136.43: 1 Dihedral angle restraints: 26164 sinusoidal: 11142 harmonic: 15022 Sorted by residual: dihedral pdb=" CA ASP O 266 " pdb=" C ASP O 266 " pdb=" N PRO O 267 " pdb=" CA PRO O 267 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN O 514 " pdb=" C ASN O 514 " pdb=" N LYS O 515 " pdb=" CA LYS O 515 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ARG B 313 " pdb=" C ARG B 313 " pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 26161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 5775 0.071 - 0.142: 761 0.142 - 0.213: 33 0.213 - 0.284: 8 0.284 - 0.355: 4 Chirality restraints: 6581 Sorted by residual: chirality pdb=" C9 4QM C 401 " pdb=" C20 4QM C 401 " pdb=" C5 4QM C 401 " pdb=" C8 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.61 2.97 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C17 4QM A2003 " pdb=" C16 4QM A2003 " pdb=" C18 4QM A2003 " pdb=" O3 4QM A2003 " both_signs ideal model delta sigma weight residual False 2.39 2.70 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C17 4QM C 401 " pdb=" C16 4QM C 401 " pdb=" C18 4QM C 401 " pdb=" O3 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.39 2.70 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 6578 not shown) Planarity restraints: 7312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU I 92 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO I 93 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO I 93 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 93 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 127 " -0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO E 128 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 128 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 128 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A1006 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C HIS A1006 " 0.034 2.00e-02 2.50e+03 pdb=" O HIS A1006 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A1007 " -0.012 2.00e-02 2.50e+03 ... (remaining 7309 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 580 2.66 - 3.22: 38363 3.22 - 3.78: 65137 3.78 - 4.34: 87845 4.34 - 4.90: 145157 Nonbonded interactions: 337082 Sorted by model distance: nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A2002 " model vdw 2.100 2.170 nonbonded pdb=" O ILE Q 122 " pdb=" OH TYR Q 127 " model vdw 2.195 2.440 nonbonded pdb=" OG SER A 980 " pdb=" OE2 GLU E 160 " model vdw 2.200 2.440 nonbonded pdb=" O PHE C 86 " pdb=" OG SER C 203 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR B 231 " pdb=" O VAL B 331 " model vdw 2.226 2.440 ... (remaining 337077 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 53 5.49 5 Mg 1 5.21 5 S 218 5.16 5 C 26533 2.51 5 N 7263 2.21 5 O 8047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 12.710 Check model and map are aligned: 0.630 Convert atoms to be neutral: 0.370 Process input model: 130.260 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 0.069 42997 Z= 0.247 Angle : 0.693 14.884 58297 Z= 0.361 Chirality : 0.047 0.355 6581 Planarity : 0.005 0.067 7312 Dihedral : 15.252 136.435 16446 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.11), residues: 5095 helix: 0.71 (0.12), residues: 1889 sheet: -0.26 (0.19), residues: 722 loop : -0.88 (0.12), residues: 2484 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 503 time to evaluate : 5.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.5541 time to fit residues: 455.8763 Evaluate side-chains 440 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 5.142 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 432 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 207 optimal weight: 0.0670 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 464 optimal weight: 0.0070 overall best weight: 2.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN B 600 HIS D 61 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 42997 Z= 0.326 Angle : 0.562 9.522 58297 Z= 0.291 Chirality : 0.043 0.159 6581 Planarity : 0.004 0.056 7312 Dihedral : 10.065 139.924 6134 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.12), residues: 5095 helix: 1.23 (0.12), residues: 1887 sheet: -0.27 (0.19), residues: 718 loop : -0.81 (0.12), residues: 2490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 459 time to evaluate : 5.111 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 23 residues processed: 469 average time/residue: 0.5457 time to fit residues: 426.6868 Evaluate side-chains 456 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 433 time to evaluate : 5.517 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3878 time to fit residues: 23.9168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 258 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 386 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 465 optimal weight: 4.9990 chunk 503 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 461 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 373 optimal weight: 0.0670 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN A 311 ASN A1021 ASN B 280 GLN B 821 HIS D 47 ASN D 61 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 132 ASN ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 42997 Z= 0.235 Angle : 0.517 9.478 58297 Z= 0.267 Chirality : 0.042 0.168 6581 Planarity : 0.003 0.052 7312 Dihedral : 10.071 142.097 6134 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.12), residues: 5095 helix: 1.41 (0.12), residues: 1891 sheet: -0.24 (0.19), residues: 720 loop : -0.75 (0.12), residues: 2484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 460 time to evaluate : 4.927 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 476 average time/residue: 0.5576 time to fit residues: 440.6777 Evaluate side-chains 441 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 430 time to evaluate : 5.148 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3969 time to fit residues: 15.0740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 460 optimal weight: 0.2980 chunk 350 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 312 optimal weight: 0.0170 chunk 467 optimal weight: 5.9990 chunk 494 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 443 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.2420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 39 ASN D 61 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 42997 Z= 0.185 Angle : 0.496 9.508 58297 Z= 0.257 Chirality : 0.041 0.165 6581 Planarity : 0.003 0.050 7312 Dihedral : 10.034 142.782 6134 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.12), residues: 5095 helix: 1.58 (0.12), residues: 1879 sheet: -0.20 (0.19), residues: 708 loop : -0.67 (0.12), residues: 2508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 451 time to evaluate : 5.275 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 466 average time/residue: 0.5802 time to fit residues: 451.0708 Evaluate side-chains 441 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 429 time to evaluate : 5.325 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4279 time to fit residues: 16.3513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 412 optimal weight: 10.0000 chunk 280 optimal weight: 0.7980 chunk 7 optimal weight: 0.0000 chunk 368 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 422 optimal weight: 3.9990 chunk 342 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 444 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 311 ASN A 695 ASN A 941 HIS A1103 GLN B1115 ASN D 61 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 42997 Z= 0.407 Angle : 0.598 10.537 58297 Z= 0.307 Chirality : 0.044 0.188 6581 Planarity : 0.004 0.049 7312 Dihedral : 10.176 143.335 6134 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.71 % Favored : 95.27 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.12), residues: 5095 helix: 1.47 (0.12), residues: 1875 sheet: -0.26 (0.20), residues: 711 loop : -0.73 (0.12), residues: 2509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 440 time to evaluate : 5.551 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 17 residues processed: 460 average time/residue: 0.5518 time to fit residues: 425.3609 Evaluate side-chains 442 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 425 time to evaluate : 5.477 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3872 time to fit residues: 19.6189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 166 optimal weight: 9.9990 chunk 445 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 290 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 495 optimal weight: 0.0970 chunk 411 optimal weight: 0.0980 chunk 229 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 260 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 695 ASN D 61 ASN ** D 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 113 GLN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 42997 Z= 0.141 Angle : 0.493 9.779 58297 Z= 0.256 Chirality : 0.041 0.171 6581 Planarity : 0.003 0.049 7312 Dihedral : 10.052 142.940 6134 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.43 (0.12), residues: 5095 helix: 1.65 (0.12), residues: 1877 sheet: -0.15 (0.20), residues: 713 loop : -0.61 (0.13), residues: 2505 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10190 Ramachandran restraints generated. 5095 Oldfield, 0 Emsley, 5095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 459 time to evaluate : 4.815 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 10 residues processed: 476 average time/residue: 0.5464 time to fit residues: 436.2234 Evaluate side-chains 445 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 435 time to evaluate : 5.428 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4191 time to fit residues: 14.8577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.222 > 50: distance: 97 - 102: 31.557 distance: 102 - 103: 48.357 distance: 103 - 106: 23.697 distance: 104 - 105: 28.686 distance: 104 - 111: 26.540 distance: 106 - 107: 18.140 distance: 107 - 108: 45.742 distance: 108 - 109: 25.995 distance: 108 - 110: 22.237 distance: 111 - 112: 34.252 distance: 112 - 113: 28.708 distance: 112 - 115: 23.162 distance: 113 - 114: 50.014 distance: 113 - 122: 34.703 distance: 115 - 116: 23.009 distance: 116 - 117: 54.683 distance: 117 - 118: 28.263 distance: 118 - 119: 34.825 distance: 119 - 120: 9.272 distance: 119 - 121: 10.707 distance: 122 - 123: 16.598 distance: 123 - 124: 33.344 distance: 123 - 126: 21.158 distance: 124 - 125: 23.998 distance: 124 - 133: 30.880 distance: 126 - 127: 11.995 distance: 127 - 128: 9.102 distance: 127 - 129: 3.625 distance: 128 - 130: 15.100 distance: 129 - 131: 12.327 distance: 130 - 132: 13.566 distance: 131 - 132: 10.377 distance: 133 - 134: 28.211 distance: 134 - 135: 30.797 distance: 134 - 137: 20.168 distance: 135 - 136: 26.554 distance: 135 - 141: 31.267 distance: 137 - 138: 20.037 distance: 138 - 139: 13.275 distance: 139 - 140: 13.518 distance: 141 - 142: 22.616 distance: 142 - 143: 20.874 distance: 142 - 145: 12.114 distance: 143 - 144: 20.190 distance: 143 - 148: 18.214 distance: 144 - 260: 33.101 distance: 145 - 146: 15.016 distance: 145 - 147: 19.288 distance: 148 - 149: 14.351 distance: 149 - 150: 39.190 distance: 149 - 152: 8.866 distance: 150 - 151: 10.598 distance: 150 - 159: 23.087 distance: 152 - 153: 17.703 distance: 153 - 154: 7.612 distance: 153 - 155: 14.798 distance: 154 - 156: 22.019 distance: 155 - 157: 23.276 distance: 156 - 158: 7.418 distance: 157 - 158: 14.359 distance: 159 - 160: 19.911 distance: 159 - 263: 19.440 distance: 160 - 161: 44.095 distance: 160 - 163: 30.791 distance: 161 - 162: 41.283 distance: 161 - 168: 6.781 distance: 162 - 274: 32.589 distance: 163 - 164: 29.817 distance: 164 - 165: 27.993 distance: 165 - 166: 5.716 distance: 165 - 167: 16.218 distance: 168 - 169: 42.048 distance: 169 - 170: 29.048 distance: 169 - 172: 6.770 distance: 170 - 171: 27.549 distance: 170 - 176: 25.787 distance: 172 - 173: 42.053 distance: 173 - 174: 35.201 distance: 173 - 175: 26.767 distance: 176 - 177: 17.797 distance: 176 - 182: 15.558 distance: 177 - 178: 19.070 distance: 177 - 180: 15.897 distance: 178 - 179: 31.997 distance: 178 - 183: 28.578 distance: 180 - 181: 44.549 distance: 181 - 182: 18.768 distance: 183 - 184: 26.768 distance: 184 - 185: 12.373 distance: 184 - 187: 13.569 distance: 185 - 190: 34.755 distance: 187 - 188: 38.099 distance: 187 - 189: 10.311