Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 22 08:24:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/08_2023/7dpa_30802.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/08_2023/7dpa_30802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/08_2023/7dpa_30802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/08_2023/7dpa_30802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/08_2023/7dpa_30802.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/08_2023/7dpa_30802.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 176 5.16 5 C 21052 2.51 5 N 5538 2.21 5 O 6092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 807": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 900": "OE1" <-> "OE2" Residue "A PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1166": "OE1" <-> "OE2" Residue "A TYR 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1237": "OE1" <-> "OE2" Residue "A TYR 1288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1336": "OE1" <-> "OE2" Residue "A GLU 1350": "OE1" <-> "OE2" Residue "A GLU 1389": "OE1" <-> "OE2" Residue "A TYR 1453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1476": "OD1" <-> "OD2" Residue "A PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "C TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "C GLU 639": "OE1" <-> "OE2" Residue "D PHE 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 807": "OE1" <-> "OE2" Residue "D GLU 835": "OE1" <-> "OE2" Residue "D GLU 900": "OE1" <-> "OE2" Residue "D PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1166": "OE1" <-> "OE2" Residue "D TYR 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1237": "OE1" <-> "OE2" Residue "D TYR 1288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1336": "OE1" <-> "OE2" Residue "D GLU 1350": "OE1" <-> "OE2" Residue "D GLU 1389": "OE1" <-> "OE2" Residue "D TYR 1453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1476": "OD1" <-> "OD2" Residue "D PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "F TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 592": "OE1" <-> "OE2" Residue "F GLU 639": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 32858 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "B" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "C" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Chain: "D" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "E" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1385 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 165} Chain: "F" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1608 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 183} Time building chain proxies: 15.08, per 1000 atoms: 0.46 Number of scatterers: 32858 At special positions: 0 Unit cell: (243.19, 163.51, 155.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 176 16.00 O 6092 8.00 N 5538 7.00 C 21052 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: 12.65 Conformation dependent library (CDL) restraints added in 4.6 seconds 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7696 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 24 sheets defined 51.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.768A pdb=" N VAL A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 removed outlier: 4.345A pdb=" N SER A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 180 through 208 Processing helix chain 'A' and resid 296 through 300 removed outlier: 4.105A pdb=" N ILE A 300 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.780A pdb=" N VAL A 337 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.820A pdb=" N ARG A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 390 through 395 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.563A pdb=" N GLY A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 429 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 518 through 524 Processing helix chain 'A' and resid 575 through 579 Processing helix chain 'A' and resid 582 through 587 Processing helix chain 'A' and resid 591 through 597 removed outlier: 3.739A pdb=" N MET A 595 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 596 " --> pdb=" O LYS A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.673A pdb=" N GLY A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 676 Processing helix chain 'A' and resid 678 through 704 removed outlier: 4.267A pdb=" N GLU A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 698 " --> pdb=" O PHE A 694 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 714 through 721 Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 745 through 751 Processing helix chain 'A' and resid 756 through 769 removed outlier: 4.148A pdb=" N PHE A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 778 through 781 Processing helix chain 'A' and resid 785 through 804 removed outlier: 3.626A pdb=" N ASN A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 818 removed outlier: 3.950A pdb=" N LYS A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 826 removed outlier: 4.446A pdb=" N ILE A 823 " --> pdb=" O TYR A 819 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 846 removed outlier: 4.203A pdb=" N SER A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 866 removed outlier: 3.771A pdb=" N ASN A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 891 removed outlier: 3.900A pdb=" N CYS A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Proline residue: A 880 - end of helix removed outlier: 4.049A pdb=" N ASP A 891 " --> pdb=" O SER A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 915 removed outlier: 4.578A pdb=" N ASP A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 943 removed outlier: 6.323A pdb=" N ARG A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG A 935 " --> pdb=" O ARG A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 964 removed outlier: 3.707A pdb=" N PHE A 953 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 970 Processing helix chain 'A' and resid 979 through 998 removed outlier: 3.998A pdb=" N PHE A 985 " --> pdb=" O ASP A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1032 removed outlier: 3.507A pdb=" N LEU A1028 " --> pdb=" O PHE A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1055 removed outlier: 4.208A pdb=" N ASN A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1064 Processing helix chain 'A' and resid 1067 through 1075 Processing helix chain 'A' and resid 1078 through 1094 removed outlier: 3.526A pdb=" N GLU A1082 " --> pdb=" O ASP A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1099 removed outlier: 4.245A pdb=" N ILE A1099 " --> pdb=" O PRO A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1114 removed outlier: 3.657A pdb=" N ILE A1109 " --> pdb=" O MET A1105 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A1111 " --> pdb=" O GLY A1107 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A1112 " --> pdb=" O PRO A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1125 Processing helix chain 'A' and resid 1126 through 1137 Processing helix chain 'A' and resid 1138 through 1142 removed outlier: 3.653A pdb=" N GLY A1142 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1162 removed outlier: 3.860A pdb=" N GLU A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1180 Processing helix chain 'A' and resid 1184 through 1215 removed outlier: 3.567A pdb=" N SER A1188 " --> pdb=" O LYS A1184 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET A1212 " --> pdb=" O ARG A1208 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1235 Processing helix chain 'A' and resid 1236 through 1255 Processing helix chain 'A' and resid 1256 through 1269 Processing helix chain 'A' and resid 1279 through 1283 removed outlier: 3.947A pdb=" N LEU A1282 " --> pdb=" O VAL A1279 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1283 " --> pdb=" O PRO A1280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1279 through 1283' Processing helix chain 'A' and resid 1292 through 1311 Processing helix chain 'A' and resid 1313 through 1332 removed outlier: 3.728A pdb=" N ALA A1317 " --> pdb=" O MET A1313 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU A1323 " --> pdb=" O LYS A1319 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1355 removed outlier: 3.565A pdb=" N ALA A1355 " --> pdb=" O ASN A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1401 Processing helix chain 'A' and resid 1447 through 1455 removed outlier: 3.928A pdb=" N LEU A1451 " --> pdb=" O PRO A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1538 Processing helix chain 'A' and resid 1544 through 1556 Processing helix chain 'A' and resid 1561 through 1570 Processing helix chain 'A' and resid 1572 through 1579 removed outlier: 3.741A pdb=" N LEU A1576 " --> pdb=" O THR A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1611 Proline residue: A1598 - end of helix Processing helix chain 'A' and resid 1615 through 1635 Processing helix chain 'B' and resid 15 through 25 removed outlier: 3.859A pdb=" N LEU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 25 " --> pdb=" O ILE B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.591A pdb=" N ARG B 66 " --> pdb=" O ASP B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 96 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 541 through 559 removed outlier: 3.768A pdb=" N LEU C 545 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 559 " --> pdb=" O ARG C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 640 Processing helix chain 'C' and resid 658 through 672 removed outlier: 3.554A pdb=" N TYR C 662 " --> pdb=" O ASP C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 696 Processing helix chain 'D' and resid 84 through 105 removed outlier: 3.769A pdb=" N VAL D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 removed outlier: 4.345A pdb=" N SER D 133 " --> pdb=" O SER D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 180 through 208 Processing helix chain 'D' and resid 296 through 300 removed outlier: 4.105A pdb=" N ILE D 300 " --> pdb=" O VAL D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.780A pdb=" N VAL D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 364 removed outlier: 3.820A pdb=" N ARG D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 387 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 404 through 412 removed outlier: 3.563A pdb=" N GLY D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 429 Processing helix chain 'D' and resid 491 through 495 Processing helix chain 'D' and resid 518 through 524 Processing helix chain 'D' and resid 575 through 579 Processing helix chain 'D' and resid 582 through 587 Processing helix chain 'D' and resid 591 through 597 removed outlier: 3.738A pdb=" N MET D 595 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU D 596 " --> pdb=" O LYS D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.673A pdb=" N GLY D 639 " --> pdb=" O VAL D 635 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 676 Processing helix chain 'D' and resid 678 through 704 removed outlier: 4.266A pdb=" N GLU D 682 " --> pdb=" O ASN D 678 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL D 698 " --> pdb=" O PHE D 694 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 714 through 721 Processing helix chain 'D' and resid 727 through 740 Processing helix chain 'D' and resid 745 through 751 Processing helix chain 'D' and resid 756 through 769 removed outlier: 4.148A pdb=" N PHE D 764 " --> pdb=" O LEU D 760 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 769 through 777 Processing helix chain 'D' and resid 778 through 781 Processing helix chain 'D' and resid 785 through 804 removed outlier: 3.626A pdb=" N ASN D 789 " --> pdb=" O ASP D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 818 removed outlier: 3.950A pdb=" N LYS D 818 " --> pdb=" O GLY D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 826 removed outlier: 4.447A pdb=" N ILE D 823 " --> pdb=" O TYR D 819 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 824 " --> pdb=" O LEU D 820 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP D 826 " --> pdb=" O SER D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 846 removed outlier: 4.203A pdb=" N SER D 846 " --> pdb=" O LYS D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 854 through 866 removed outlier: 3.772A pdb=" N ASN D 858 " --> pdb=" O ARG D 854 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 866 " --> pdb=" O LYS D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 891 removed outlier: 3.901A pdb=" N CYS D 874 " --> pdb=" O ARG D 870 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N GLU D 876 " --> pdb=" O SER D 872 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 877 " --> pdb=" O GLU D 873 " (cutoff:3.500A) Proline residue: D 880 - end of helix removed outlier: 4.049A pdb=" N ASP D 891 " --> pdb=" O SER D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 915 removed outlier: 4.577A pdb=" N ASP D 898 " --> pdb=" O SER D 894 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU D 900 " --> pdb=" O LYS D 896 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 943 removed outlier: 6.323A pdb=" N ARG D 934 " --> pdb=" O GLU D 930 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG D 935 " --> pdb=" O ARG D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 949 through 964 removed outlier: 3.707A pdb=" N PHE D 953 " --> pdb=" O HIS D 949 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET D 964 " --> pdb=" O LEU D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 979 through 998 removed outlier: 3.997A pdb=" N PHE D 985 " --> pdb=" O ASP D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1032 removed outlier: 3.507A pdb=" N LEU D1028 " --> pdb=" O PHE D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1055 removed outlier: 4.208A pdb=" N ASN D1045 " --> pdb=" O GLN D1041 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1064 Processing helix chain 'D' and resid 1067 through 1075 Processing helix chain 'D' and resid 1078 through 1094 removed outlier: 3.525A pdb=" N GLU D1082 " --> pdb=" O ASP D1078 " (cutoff:3.500A) Processing helix chain 'D' and resid 1095 through 1099 removed outlier: 4.246A pdb=" N ILE D1099 " --> pdb=" O PRO D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1105 through 1114 removed outlier: 3.657A pdb=" N ILE D1109 " --> pdb=" O MET D1105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D1110 " --> pdb=" O VAL D1106 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU D1111 " --> pdb=" O GLY D1107 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D1112 " --> pdb=" O PRO D1108 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1125 Processing helix chain 'D' and resid 1126 through 1137 Processing helix chain 'D' and resid 1138 through 1142 removed outlier: 3.653A pdb=" N GLY D1142 " --> pdb=" O SER D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1162 removed outlier: 3.860A pdb=" N GLU D1150 " --> pdb=" O MET D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1165 through 1180 Processing helix chain 'D' and resid 1184 through 1215 removed outlier: 3.567A pdb=" N SER D1188 " --> pdb=" O LYS D1184 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET D1212 " --> pdb=" O ARG D1208 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU D1215 " --> pdb=" O ILE D1211 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1235 Processing helix chain 'D' and resid 1236 through 1255 Processing helix chain 'D' and resid 1256 through 1269 Processing helix chain 'D' and resid 1279 through 1283 removed outlier: 3.946A pdb=" N LEU D1282 " --> pdb=" O VAL D1279 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D1283 " --> pdb=" O PRO D1280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1279 through 1283' Processing helix chain 'D' and resid 1292 through 1311 Processing helix chain 'D' and resid 1313 through 1332 removed outlier: 3.729A pdb=" N ALA D1317 " --> pdb=" O MET D1313 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU D1323 " --> pdb=" O LYS D1319 " (cutoff:3.500A) Processing helix chain 'D' and resid 1334 through 1355 removed outlier: 3.565A pdb=" N ALA D1355 " --> pdb=" O ASN D1351 " (cutoff:3.500A) Processing helix chain 'D' and resid 1390 through 1401 Processing helix chain 'D' and resid 1447 through 1455 removed outlier: 3.927A pdb=" N LEU D1451 " --> pdb=" O PRO D1447 " (cutoff:3.500A) Processing helix chain 'D' and resid 1513 through 1538 Processing helix chain 'D' and resid 1544 through 1556 Processing helix chain 'D' and resid 1561 through 1570 Processing helix chain 'D' and resid 1572 through 1579 removed outlier: 3.741A pdb=" N LEU D1576 " --> pdb=" O THR D1572 " (cutoff:3.500A) Processing helix chain 'D' and resid 1584 through 1611 Proline residue: D1598 - end of helix Processing helix chain 'D' and resid 1615 through 1635 Processing helix chain 'E' and resid 15 through 25 removed outlier: 3.859A pdb=" N LEU E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 25 " --> pdb=" O ILE E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.591A pdb=" N ARG E 66 " --> pdb=" O ASP E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 96 Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'F' and resid 531 through 540 Processing helix chain 'F' and resid 541 through 559 removed outlier: 3.768A pdb=" N LEU F 545 " --> pdb=" O GLN F 541 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU F 546 " --> pdb=" O PRO F 542 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 637 through 640 Processing helix chain 'F' and resid 658 through 672 removed outlier: 3.554A pdb=" N TYR F 662 " --> pdb=" O ASP F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 696 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 234 removed outlier: 7.424A pdb=" N PHE A 228 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 245 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A 234 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 239 " --> pdb=" O ASN A 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 3.588A pdb=" N GLU A 307 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS A 305 " --> pdb=" O TRP A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 474 removed outlier: 3.776A pdb=" N SER A 471 " --> pdb=" O ARG A 528 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 548 through 549 removed outlier: 3.600A pdb=" N VAL A 549 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A 572 " --> pdb=" O VAL A 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1362 through 1363 removed outlier: 4.371A pdb=" N TYR A1362 " --> pdb=" O VAL A1431 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN A1460 " --> pdb=" O THR A1491 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1365 through 1366 Processing sheet with id=AA8, first strand: chain 'A' and resid 1467 through 1469 Processing sheet with id=AA9, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.520A pdb=" N VAL B 8 " --> pdb=" O TRP B 56 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL B 7 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS B 81 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 9 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N SER B 83 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B 78 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL B 113 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE B 80 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N THR B 115 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N PHE B 82 " --> pdb=" O THR B 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 576 through 579 removed outlier: 4.646A pdb=" N TYR C 576 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 589 " --> pdb=" O TYR C 576 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 616 through 618 removed outlier: 4.676A pdb=" N PHE C 642 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 654 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 652 " --> pdb=" O ILE C 644 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR C 646 " --> pdb=" O CYS C 650 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS C 650 " --> pdb=" O TYR C 646 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB5, first strand: chain 'D' and resid 228 through 234 removed outlier: 7.425A pdb=" N PHE D 228 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU D 245 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN D 234 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA D 239 " --> pdb=" O ASN D 234 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 269 through 272 removed outlier: 3.587A pdb=" N GLU D 307 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS D 305 " --> pdb=" O TRP D 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 469 through 474 removed outlier: 3.777A pdb=" N SER D 471 " --> pdb=" O ARG D 528 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 548 through 549 removed outlier: 3.600A pdb=" N VAL D 549 " --> pdb=" O TYR D 572 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR D 572 " --> pdb=" O VAL D 549 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 1362 through 1363 removed outlier: 4.371A pdb=" N TYR D1362 " --> pdb=" O VAL D1431 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN D1460 " --> pdb=" O THR D1491 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 1365 through 1366 Processing sheet with id=AC2, first strand: chain 'D' and resid 1467 through 1469 Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'E' and resid 56 through 57 removed outlier: 3.520A pdb=" N VAL E 8 " --> pdb=" O TRP E 56 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL E 7 " --> pdb=" O LEU E 79 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N CYS E 81 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL E 9 " --> pdb=" O CYS E 81 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER E 83 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 78 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL E 113 " --> pdb=" O PHE E 78 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE E 80 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR E 115 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE E 82 " --> pdb=" O THR E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 576 through 579 removed outlier: 4.646A pdb=" N TYR F 576 " --> pdb=" O GLY F 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY F 589 " --> pdb=" O TYR F 576 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 616 through 618 removed outlier: 4.676A pdb=" N PHE F 642 " --> pdb=" O PHE F 654 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE F 654 " --> pdb=" O PHE F 642 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU F 652 " --> pdb=" O ILE F 644 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR F 646 " --> pdb=" O CYS F 650 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS F 650 " --> pdb=" O TYR F 646 " (cutoff:3.500A) 1444 hydrogen bonds defined for protein. 4230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.78 Time building geometry restraints manager: 13.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9652 1.33 - 1.45: 5087 1.45 - 1.57: 18521 1.57 - 1.69: 2 1.69 - 1.81: 294 Bond restraints: 33556 Sorted by residual: bond pdb=" CB TYR D1301 " pdb=" CG TYR D1301 " ideal model delta sigma weight residual 1.512 1.470 0.042 2.20e-02 2.07e+03 3.63e+00 bond pdb=" CB TYR A1301 " pdb=" CG TYR A1301 " ideal model delta sigma weight residual 1.512 1.471 0.041 2.20e-02 2.07e+03 3.53e+00 bond pdb=" CB PHE A1308 " pdb=" CG PHE A1308 " ideal model delta sigma weight residual 1.502 1.459 0.043 2.30e-02 1.89e+03 3.43e+00 bond pdb=" CG1 ILE A1125 " pdb=" CD1 ILE A1125 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.39e+00 bond pdb=" CB PHE D1308 " pdb=" CG PHE D1308 " ideal model delta sigma weight residual 1.502 1.460 0.042 2.30e-02 1.89e+03 3.37e+00 ... (remaining 33551 not shown) Histogram of bond angle deviations from ideal: 96.79 - 104.29: 497 104.29 - 111.80: 15305 111.80 - 119.30: 12511 119.30 - 126.80: 16640 126.80 - 134.31: 371 Bond angle restraints: 45324 Sorted by residual: angle pdb=" CG1 ILE D 101 " pdb=" CB ILE D 101 " pdb=" CG2 ILE D 101 " ideal model delta sigma weight residual 110.70 96.79 13.91 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CG1 ILE A 101 " pdb=" CB ILE A 101 " pdb=" CG2 ILE A 101 " ideal model delta sigma weight residual 110.70 96.82 13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CA PRO D1514 " pdb=" N PRO D1514 " pdb=" CD PRO D1514 " ideal model delta sigma weight residual 112.00 106.10 5.90 1.40e+00 5.10e-01 1.78e+01 angle pdb=" CA PRO A1514 " pdb=" N PRO A1514 " pdb=" CD PRO A1514 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" C ARG D 157 " pdb=" N MET D 158 " pdb=" CA MET D 158 " ideal model delta sigma weight residual 121.18 113.42 7.76 1.98e+00 2.55e-01 1.54e+01 ... (remaining 45319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 18000 17.74 - 35.48: 2022 35.48 - 53.21: 362 53.21 - 70.95: 52 70.95 - 88.69: 40 Dihedral angle restraints: 20476 sinusoidal: 8586 harmonic: 11890 Sorted by residual: dihedral pdb=" CA LEU D 820 " pdb=" C LEU D 820 " pdb=" N PRO D 821 " pdb=" CA PRO D 821 " ideal model delta harmonic sigma weight residual -180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LEU A 820 " pdb=" C LEU A 820 " pdb=" N PRO A 821 " pdb=" CA PRO A 821 " ideal model delta harmonic sigma weight residual 180.00 -150.58 -29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN F 541 " pdb=" C GLN F 541 " pdb=" N PRO F 542 " pdb=" CA PRO F 542 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 20473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3846 0.057 - 0.115: 1028 0.115 - 0.172: 126 0.172 - 0.230: 20 0.230 - 0.287: 4 Chirality restraints: 5024 Sorted by residual: chirality pdb=" CG LEU A1342 " pdb=" CB LEU A1342 " pdb=" CD1 LEU A1342 " pdb=" CD2 LEU A1342 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CG LEU D1342 " pdb=" CB LEU D1342 " pdb=" CD1 LEU D1342 " pdb=" CD2 LEU D1342 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR D1291 " pdb=" N TYR D1291 " pdb=" C TYR D1291 " pdb=" CB TYR D1291 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 5021 not shown) Planarity restraints: 5796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 665 " -0.026 2.00e-02 2.50e+03 2.70e-02 1.82e+01 pdb=" CG TRP C 665 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP C 665 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 665 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 665 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 665 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 665 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 665 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 665 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 665 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 665 " 0.025 2.00e-02 2.50e+03 2.69e-02 1.81e+01 pdb=" CG TRP F 665 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP F 665 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP F 665 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 665 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 665 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP F 665 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 665 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 665 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP F 665 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D1513 " 0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO D1514 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO D1514 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D1514 " 0.055 5.00e-02 4.00e+02 ... (remaining 5793 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 411 2.61 - 3.18: 31081 3.18 - 3.76: 51128 3.76 - 4.33: 69157 4.33 - 4.90: 108564 Nonbonded interactions: 260341 Sorted by model distance: nonbonded pdb=" OG1 THR A 180 " pdb=" OE1 GLN A 962 " model vdw 2.038 2.440 nonbonded pdb=" OG1 THR D 180 " pdb=" OE1 GLN D 962 " model vdw 2.038 2.440 nonbonded pdb=" O ASP D1275 " pdb=" OG1 THR D1292 " model vdw 2.064 2.440 nonbonded pdb=" O ASP A1275 " pdb=" OG1 THR A1292 " model vdw 2.065 2.440 nonbonded pdb=" O LEU D1059 " pdb=" OG1 THR D1063 " model vdw 2.067 2.440 ... (remaining 260336 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 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 31.430 Check model and map are aligned: 0.590 Set scattering table: 0.270 Process input model: 78.950 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 33556 Z= 0.361 Angle : 0.845 13.910 45324 Z= 0.459 Chirality : 0.051 0.287 5024 Planarity : 0.006 0.100 5796 Dihedral : 15.299 88.688 12780 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % 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: -3.05 (0.12), residues: 4022 helix: -1.34 (0.11), residues: 1816 sheet: -2.35 (0.30), residues: 262 loop : -2.65 (0.13), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 369 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.4860 time to fit residues: 285.3603 Evaluate side-chains 212 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.901 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 337 optimal weight: 0.8980 chunk 303 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 103 optimal weight: 0.0670 chunk 204 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 chunk 313 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 190 optimal weight: 7.9990 chunk 233 optimal weight: 30.0000 chunk 363 optimal weight: 2.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS ** A 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN A1272 GLN A1545 HIS ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN D 278 GLN D 394 HIS ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 946 GLN D1272 GLN D1545 HIS ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4073 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 33556 Z= 0.217 Angle : 0.747 11.229 45324 Z= 0.386 Chirality : 0.046 0.256 5024 Planarity : 0.005 0.072 5796 Dihedral : 6.113 34.027 4394 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -2.54 (0.12), residues: 4022 helix: -0.78 (0.11), residues: 1876 sheet: -2.31 (0.29), residues: 278 loop : -2.54 (0.14), residues: 1868 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 262 average time/residue: 0.4643 time to fit residues: 200.9457 Evaluate side-chains 220 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 3.852 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3246 time to fit residues: 15.9252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 0.0570 chunk 112 optimal weight: 0.8980 chunk 302 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 363 optimal weight: 9.9990 chunk 393 optimal weight: 20.0000 chunk 324 optimal weight: 3.9990 chunk 360 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 171 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 825 ASN D1272 GLN ** D1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4127 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 33556 Z= 0.213 Angle : 0.689 10.377 45324 Z= 0.355 Chirality : 0.044 0.280 5024 Planarity : 0.005 0.072 5796 Dihedral : 5.796 34.461 4394 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -2.10 (0.13), residues: 4022 helix: -0.45 (0.11), residues: 1882 sheet: -2.14 (0.29), residues: 278 loop : -2.27 (0.14), residues: 1862 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 4.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 247 average time/residue: 0.4740 time to fit residues: 198.0856 Evaluate side-chains 211 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 4.031 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3286 time to fit residues: 15.6858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 359 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 188 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 365 optimal weight: 10.0000 chunk 386 optimal weight: 0.2980 chunk 190 optimal weight: 7.9990 chunk 346 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1535 GLN ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 GLN ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 GLN ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4269 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 33556 Z= 0.293 Angle : 0.730 12.979 45324 Z= 0.377 Chirality : 0.045 0.297 5024 Planarity : 0.005 0.073 5796 Dihedral : 5.773 36.766 4394 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -2.12 (0.13), residues: 4022 helix: -0.48 (0.11), residues: 1858 sheet: -2.11 (0.31), residues: 234 loop : -2.27 (0.14), residues: 1930 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 189 time to evaluate : 3.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 40 residues processed: 261 average time/residue: 0.4482 time to fit residues: 199.2045 Evaluate side-chains 223 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 183 time to evaluate : 3.653 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3319 time to fit residues: 30.3565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 287 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 329 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 347 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 799 ASN ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1535 GLN ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4266 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 33556 Z= 0.254 Angle : 0.698 13.553 45324 Z= 0.360 Chirality : 0.045 0.277 5024 Planarity : 0.005 0.065 5796 Dihedral : 5.663 35.371 4394 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.95 (0.13), residues: 4022 helix: -0.37 (0.11), residues: 1890 sheet: -1.88 (0.30), residues: 258 loop : -2.19 (0.14), residues: 1874 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 18 residues processed: 229 average time/residue: 0.4481 time to fit residues: 175.1295 Evaluate side-chains 192 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 3.832 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3089 time to fit residues: 16.1040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 2.9990 chunk 348 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 387 optimal weight: 4.9990 chunk 321 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 GLN ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 ASN ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1535 GLN ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1583 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4295 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 33556 Z= 0.260 Angle : 0.705 12.372 45324 Z= 0.362 Chirality : 0.044 0.327 5024 Planarity : 0.005 0.114 5796 Dihedral : 5.618 35.943 4394 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 25.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.87 (0.13), residues: 4022 helix: -0.30 (0.11), residues: 1886 sheet: -1.61 (0.29), residues: 284 loop : -2.19 (0.14), residues: 1852 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 174 time to evaluate : 4.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 27 residues processed: 230 average time/residue: 0.4305 time to fit residues: 171.3999 Evaluate side-chains 198 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 4.401 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3477 time to fit residues: 23.4582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 10.0000 chunk 43 optimal weight: 0.0010 chunk 220 optimal weight: 8.9990 chunk 282 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 325 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 385 optimal weight: 5.9990 chunk 241 optimal weight: 40.0000 chunk 235 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1535 GLN ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1596 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4245 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 33556 Z= 0.205 Angle : 0.695 13.460 45324 Z= 0.350 Chirality : 0.044 0.306 5024 Planarity : 0.005 0.117 5796 Dihedral : 5.524 34.550 4394 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.67 (0.13), residues: 4022 helix: -0.11 (0.11), residues: 1880 sheet: -1.49 (0.29), residues: 292 loop : -2.11 (0.14), residues: 1850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 187 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 10 residues processed: 222 average time/residue: 0.4313 time to fit residues: 168.4281 Evaluate side-chains 186 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 4.300 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3104 time to fit residues: 11.3551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 0.0060 chunk 74 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 190 optimal weight: 0.0370 chunk 35 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 799 ASN D1535 GLN ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1596 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4224 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 33556 Z= 0.197 Angle : 0.705 12.311 45324 Z= 0.354 Chirality : 0.044 0.352 5024 Planarity : 0.005 0.111 5796 Dihedral : 5.431 33.825 4394 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.66 (0.13), residues: 4022 helix: -0.04 (0.11), residues: 1890 sheet: -1.59 (0.29), residues: 300 loop : -2.16 (0.14), residues: 1832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 4.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 200 average time/residue: 0.4265 time to fit residues: 149.3602 Evaluate side-chains 184 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 4.017 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3478 time to fit residues: 10.0345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 1.9990 chunk 369 optimal weight: 8.9990 chunk 336 optimal weight: 0.8980 chunk 359 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 282 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 324 optimal weight: 0.9980 chunk 339 optimal weight: 0.9980 chunk 358 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 HIS C 571 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4201 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 33556 Z= 0.188 Angle : 0.694 13.642 45324 Z= 0.348 Chirality : 0.044 0.375 5024 Planarity : 0.005 0.108 5796 Dihedral : 5.339 33.354 4394 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.50 (0.13), residues: 4022 helix: 0.04 (0.11), residues: 1906 sheet: -1.53 (0.29), residues: 322 loop : -2.04 (0.15), residues: 1794 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 190 time to evaluate : 4.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 199 average time/residue: 0.4181 time to fit residues: 146.3398 Evaluate side-chains 184 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 3.944 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3103 time to fit residues: 7.6059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 1.9990 chunk 379 optimal weight: 3.9990 chunk 231 optimal weight: 20.0000 chunk 180 optimal weight: 0.7980 chunk 264 optimal weight: 0.0470 chunk 398 optimal weight: 8.9990 chunk 366 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4223 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 33556 Z= 0.200 Angle : 0.716 16.334 45324 Z= 0.356 Chirality : 0.044 0.328 5024 Planarity : 0.005 0.112 5796 Dihedral : 5.283 33.416 4394 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.43 (0.13), residues: 4022 helix: 0.07 (0.12), residues: 1896 sheet: -1.48 (0.29), residues: 322 loop : -1.97 (0.15), residues: 1804 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8044 Ramachandran restraints generated. 4022 Oldfield, 0 Emsley, 4022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 190 average time/residue: 0.4365 time to fit residues: 144.8590 Evaluate side-chains 183 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 180 time to evaluate : 4.454 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3498 time to fit residues: 7.4571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 6.9990 chunk 338 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 292 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 88 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 326 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.0370 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1535 GLN ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.072404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.045885 restraints weight = 223980.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.046549 restraints weight = 160597.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.046927 restraints weight = 129644.829| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 33556 Z= 0.176 Angle : 0.709 17.431 45324 Z= 0.348 Chirality : 0.044 0.346 5024 Planarity : 0.005 0.104 5796 Dihedral : 5.184 32.028 4394 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % 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: -1.30 (0.13), residues: 4022 helix: 0.24 (0.12), residues: 1888 sheet: -1.46 (0.28), residues: 318 loop : -1.96 (0.15), residues: 1816 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6908.03 seconds wall clock time: 127 minutes 52.60 seconds (7672.60 seconds total)