Starting phenix.real_space_refine on Fri Mar 22 08:48:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/03_2024/7dpa_30802.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/03_2024/7dpa_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_30802/03_2024/7dpa_30802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/03_2024/7dpa_30802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/03_2024/7dpa_30802.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dpa_30802/03_2024/7dpa_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-dev-5265/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: 16.09, per 1000 atoms: 0.49 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: 12.99 Conformation dependent library (CDL) restraints added in 5.5 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: 3.57 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: 11.35 Time building geometry restraints manager: 13.77 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: 13.810 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 30.060 Check model and map are aligned: 0.610 Set scattering table: 0.310 Process input model: 79.940 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.170 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.380 ------------------------------------------------------------------------------- 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 % Allowed : 0.35 % Favored : 99.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP C 665 HIS 0.014 0.002 HIS D 924 PHE 0.053 0.002 PHE A1308 TYR 0.045 0.002 TYR A1262 ARG 0.010 0.001 ARG F 683 *********************** 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 : 4.174 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 REVERT: A 120 MET cc_start: 0.6732 (mmt) cc_final: 0.5802 (mmt) REVERT: A 353 MET cc_start: 0.0915 (mmt) cc_final: 0.0590 (mmp) REVERT: A 364 MET cc_start: 0.1966 (mtt) cc_final: 0.1691 (pmm) REVERT: A 595 MET cc_start: -0.2710 (mtt) cc_final: -0.3137 (mmt) REVERT: D 120 MET cc_start: 0.6504 (mmt) cc_final: 0.6042 (mmt) REVERT: D 306 MET cc_start: -0.1039 (pmm) cc_final: -0.2848 (ptm) REVERT: D 353 MET cc_start: 0.0562 (mmt) cc_final: 0.0341 (mmp) REVERT: D 364 MET cc_start: 0.1593 (mtt) cc_final: 0.1173 (pmm) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.4693 time to fit residues: 274.8160 Evaluate side-chains 212 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 4.264 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 278 GLN ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN D 908 ASN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4077 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33556 Z= 0.223 Angle : 0.737 11.160 45324 Z= 0.380 Chirality : 0.046 0.322 5024 Planarity : 0.005 0.071 5796 Dihedral : 6.088 33.380 4394 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 0.87 % Allowed : 10.68 % Favored : 88.45 % 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: -2.52 (0.12), residues: 4022 helix: -0.77 (0.11), residues: 1880 sheet: -2.33 (0.29), residues: 278 loop : -2.53 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 665 HIS 0.014 0.002 HIS D 394 PHE 0.021 0.002 PHE D 798 TYR 0.022 0.001 TYR A 969 ARG 0.008 0.000 ARG A 103 *********************** 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 271 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 239 time to evaluate : 4.052 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: A 40 MET cc_start: 0.4112 (tpp) cc_final: 0.3847 (tpp) REVERT: A 353 MET cc_start: 0.0808 (mmt) cc_final: 0.0120 (mmp) REVERT: A 364 MET cc_start: 0.2004 (mtt) cc_final: 0.1690 (pmm) REVERT: A 595 MET cc_start: -0.2822 (mtt) cc_final: -0.3186 (mmt) REVERT: D 40 MET cc_start: 0.4039 (tpp) cc_final: 0.3578 (tpp) REVERT: D 306 MET cc_start: -0.1196 (pmm) cc_final: -0.2923 (ptm) REVERT: D 353 MET cc_start: 0.0680 (mmt) cc_final: 0.0031 (mmp) REVERT: D 364 MET cc_start: 0.1559 (mtt) cc_final: 0.1181 (pmm) outliers start: 32 outliers final: 18 residues processed: 264 average time/residue: 0.4482 time to fit residues: 193.8965 Evaluate side-chains 222 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 1272 GLN Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 1272 GLN Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 201 optimal weight: 3.9990 chunk 112 optimal weight: 0.3980 chunk 302 optimal weight: 7.9990 chunk 247 optimal weight: 5.9990 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: 0.9990 chunk 124 optimal weight: 2.9990 chunk 291 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 171 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 GLN D 825 ASN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4180 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33556 Z= 0.244 Angle : 0.704 10.443 45324 Z= 0.364 Chirality : 0.044 0.256 5024 Planarity : 0.005 0.072 5796 Dihedral : 5.819 35.911 4394 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 1.77 % Allowed : 13.76 % Favored : 84.46 % 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: -2.20 (0.13), residues: 4022 helix: -0.54 (0.11), residues: 1892 sheet: -2.11 (0.28), residues: 286 loop : -2.34 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 56 HIS 0.010 0.001 HIS A 394 PHE 0.019 0.001 PHE A 59 TYR 0.019 0.001 TYR D 258 ARG 0.007 0.000 ARG D1627 *********************** 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 268 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 203 time to evaluate : 3.726 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: A 353 MET cc_start: 0.0759 (mmt) cc_final: 0.0208 (mmp) REVERT: A 364 MET cc_start: 0.2215 (mtt) cc_final: 0.1774 (pmm) REVERT: A 595 MET cc_start: -0.2725 (mtt) cc_final: -0.3026 (mmt) REVERT: A 1474 ASP cc_start: 0.2713 (OUTLIER) cc_final: 0.2423 (p0) REVERT: D 40 MET cc_start: 0.4327 (tpp) cc_final: 0.3955 (tpp) REVERT: D 306 MET cc_start: -0.1411 (pmm) cc_final: -0.3314 (ptm) REVERT: D 327 MET cc_start: 0.0345 (pmm) cc_final: 0.0041 (ptm) REVERT: D 353 MET cc_start: 0.0863 (mmt) cc_final: 0.0300 (mmp) REVERT: D 364 MET cc_start: 0.1733 (mtt) cc_final: 0.1372 (pmm) REVERT: D 1474 ASP cc_start: 0.2970 (OUTLIER) cc_final: 0.2662 (p0) outliers start: 65 outliers final: 38 residues processed: 254 average time/residue: 0.4253 time to fit residues: 181.5774 Evaluate side-chains 232 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 192 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1064 PHE Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1112 VAL Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1520 GLU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR 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: 9.9990 chunk 188 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 244 optimal weight: 0.3980 chunk 365 optimal weight: 8.9990 chunk 386 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 346 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 743 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4165 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33556 Z= 0.208 Angle : 0.678 11.950 45324 Z= 0.346 Chirality : 0.044 0.311 5024 Planarity : 0.004 0.066 5796 Dihedral : 5.643 35.636 4394 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 2.57 % Allowed : 14.28 % Favored : 83.15 % 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: -1.92 (0.13), residues: 4022 helix: -0.29 (0.11), residues: 1888 sheet: -2.08 (0.29), residues: 278 loop : -2.19 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 56 HIS 0.008 0.001 HIS D 711 PHE 0.019 0.001 PHE D1064 TYR 0.018 0.001 TYR A 258 ARG 0.003 0.000 ARG A 875 *********************** 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 290 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 196 time to evaluate : 3.860 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: A 1 MET cc_start: 0.1298 (mmt) cc_final: 0.0843 (mmp) REVERT: A 353 MET cc_start: 0.0975 (mmt) cc_final: 0.0338 (mmp) REVERT: A 364 MET cc_start: 0.2315 (mtt) cc_final: 0.1751 (pmm) REVERT: A 595 MET cc_start: -0.2733 (mtt) cc_final: -0.2977 (mmt) REVERT: A 1474 ASP cc_start: 0.2932 (OUTLIER) cc_final: 0.2629 (p0) REVERT: A 1531 ASN cc_start: 0.6496 (p0) cc_final: 0.6285 (p0) REVERT: B 145 MET cc_start: 0.4843 (tpt) cc_final: 0.4587 (mmm) REVERT: C 720 TYR cc_start: 0.0850 (OUTLIER) cc_final: -0.0027 (t80) REVERT: D 40 MET cc_start: 0.4417 (tpp) cc_final: 0.4084 (tpp) REVERT: D 306 MET cc_start: -0.1371 (pmm) cc_final: -0.4433 (ptm) REVERT: D 327 MET cc_start: 0.0346 (pmm) cc_final: -0.0097 (ptm) REVERT: D 353 MET cc_start: 0.0812 (mmt) cc_final: 0.0227 (mmp) REVERT: D 364 MET cc_start: 0.2123 (mtt) cc_final: 0.1839 (pmm) REVERT: D 1102 ILE cc_start: 0.6625 (OUTLIER) cc_final: 0.5935 (mt) REVERT: D 1474 ASP cc_start: 0.3035 (OUTLIER) cc_final: 0.2741 (p0) REVERT: D 1531 ASN cc_start: 0.6423 (p0) cc_final: 0.6212 (p0) REVERT: F 720 TYR cc_start: 0.0736 (OUTLIER) cc_final: 0.0040 (t80) outliers start: 94 outliers final: 50 residues processed: 275 average time/residue: 0.4107 time to fit residues: 192.1704 Evaluate side-chains 243 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 929 MET Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 1065 SER Chi-restraints excluded: chain D residue 1102 ILE Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1499 LEU Chi-restraints excluded: chain D residue 1520 GLU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 322 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 159 optimal weight: 8.9990 chunk 329 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 347 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN A 799 ASN A1535 GLN ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1596 GLN ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 ASN ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4278 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33556 Z= 0.277 Angle : 0.714 14.537 45324 Z= 0.367 Chirality : 0.045 0.303 5024 Planarity : 0.005 0.113 5796 Dihedral : 5.643 36.602 4394 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 24.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.87 % Allowed : 15.70 % Favored : 81.43 % 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: -1.96 (0.13), residues: 4022 helix: -0.33 (0.11), residues: 1884 sheet: -1.89 (0.30), residues: 258 loop : -2.25 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 56 HIS 0.008 0.001 HIS D 154 PHE 0.018 0.002 PHE D 59 TYR 0.019 0.002 TYR D 258 ARG 0.013 0.001 ARG A 931 *********************** 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 287 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 182 time to evaluate : 3.791 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: A 364 MET cc_start: 0.2591 (mtt) cc_final: 0.2271 (pmm) REVERT: A 595 MET cc_start: -0.2680 (mtt) cc_final: -0.2979 (mmt) REVERT: A 737 LEU cc_start: -0.0252 (OUTLIER) cc_final: -0.0533 (mt) REVERT: A 1474 ASP cc_start: 0.3275 (OUTLIER) cc_final: 0.2873 (p0) REVERT: B 145 MET cc_start: 0.5092 (tpt) cc_final: 0.4807 (mmm) REVERT: D 40 MET cc_start: 0.4261 (tpp) cc_final: 0.3976 (tpp) REVERT: D 327 MET cc_start: 0.0355 (pmm) cc_final: -0.0128 (ptm) REVERT: D 364 MET cc_start: 0.2302 (mtt) cc_final: 0.1708 (mpp) REVERT: D 964 MET cc_start: 0.6454 (ptp) cc_final: 0.5996 (ptp) REVERT: D 1131 MET cc_start: 0.6873 (OUTLIER) cc_final: 0.6534 (mtm) REVERT: D 1474 ASP cc_start: 0.3339 (OUTLIER) cc_final: 0.2974 (p0) outliers start: 105 outliers final: 64 residues processed: 275 average time/residue: 0.4202 time to fit residues: 195.8499 Evaluate side-chains 241 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 173 time to evaluate : 4.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1112 VAL Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 975 THR Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1065 SER Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1499 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 130 optimal weight: 0.9980 chunk 348 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 387 optimal weight: 7.9990 chunk 321 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 203 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1535 GLN ** 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 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4168 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33556 Z= 0.184 Angle : 0.677 14.038 45324 Z= 0.341 Chirality : 0.044 0.266 5024 Planarity : 0.004 0.096 5796 Dihedral : 5.434 33.811 4394 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.18 % Allowed : 17.39 % Favored : 80.42 % 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: -0.01 (0.11), residues: 1890 sheet: -1.93 (0.27), residues: 326 loop : -2.13 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1538 HIS 0.007 0.001 HIS D 711 PHE 0.015 0.001 PHE D 798 TYR 0.016 0.001 TYR D 258 ARG 0.010 0.000 ARG A 96 *********************** 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 266 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 186 time to evaluate : 4.049 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: A 40 MET cc_start: 0.3910 (tpp) cc_final: 0.3544 (tpp) REVERT: A 595 MET cc_start: -0.2772 (mtt) cc_final: -0.2998 (mmt) REVERT: A 1474 ASP cc_start: 0.3355 (OUTLIER) cc_final: 0.2990 (p0) REVERT: B 145 MET cc_start: 0.5346 (tpt) cc_final: 0.5089 (mmm) REVERT: C 720 TYR cc_start: 0.1024 (OUTLIER) cc_final: 0.0115 (t80) REVERT: D 1 MET cc_start: 0.1188 (mmt) cc_final: 0.0625 (mmp) REVERT: D 327 MET cc_start: 0.0492 (pmm) cc_final: 0.0114 (ptm) REVERT: D 364 MET cc_start: 0.2266 (mtt) cc_final: 0.1695 (mpp) REVERT: D 1131 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6426 (mtm) REVERT: D 1406 GLU cc_start: 0.4216 (OUTLIER) cc_final: 0.2885 (pm20) REVERT: D 1474 ASP cc_start: 0.3247 (OUTLIER) cc_final: 0.2879 (p0) REVERT: F 720 TYR cc_start: 0.0612 (OUTLIER) cc_final: 0.0008 (t80) outliers start: 80 outliers final: 48 residues processed: 256 average time/residue: 0.4018 time to fit residues: 175.5209 Evaluate side-chains 233 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 720 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 860 MET Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1398 LEU Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 681 LEU Chi-restraints excluded: chain F residue 720 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 373 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 218 optimal weight: 0.6980 chunk 325 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 385 optimal weight: 0.9980 chunk 241 optimal weight: 50.0000 chunk 235 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1535 GLN ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 ASN ** 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: 0.4262 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33556 Z= 0.242 Angle : 0.704 15.371 45324 Z= 0.357 Chirality : 0.044 0.310 5024 Planarity : 0.005 0.142 5796 Dihedral : 5.425 35.122 4394 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 23.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.43 % Allowed : 18.16 % Favored : 79.41 % 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: -1.60 (0.13), residues: 4022 helix: -0.04 (0.11), residues: 1872 sheet: -1.58 (0.29), residues: 296 loop : -2.07 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1091 HIS 0.007 0.001 HIS D 711 PHE 0.017 0.001 PHE A 976 TYR 0.018 0.001 TYR D 258 ARG 0.009 0.000 ARG D 931 *********************** 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 262 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 173 time to evaluate : 3.944 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: A 40 MET cc_start: 0.4154 (tpp) cc_final: 0.3870 (tpp) REVERT: A 327 MET cc_start: -0.1242 (tmm) cc_final: -0.2475 (mtt) REVERT: A 595 MET cc_start: -0.2814 (mtt) cc_final: -0.3079 (mmt) REVERT: A 1406 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.3274 (pm20) REVERT: A 1474 ASP cc_start: 0.3444 (OUTLIER) cc_final: 0.3019 (p0) REVERT: A 1549 MET cc_start: 0.5021 (mmm) cc_final: 0.4818 (mmm) REVERT: B 145 MET cc_start: 0.5250 (tpt) cc_final: 0.4975 (mmm) REVERT: D 1 MET cc_start: 0.1273 (mmt) cc_final: 0.0958 (mmp) REVERT: D 327 MET cc_start: 0.0561 (pmm) cc_final: 0.0173 (ptm) REVERT: D 364 MET cc_start: 0.2436 (mtt) cc_final: 0.2047 (mpp) REVERT: D 680 MET cc_start: 0.3150 (ppp) cc_final: 0.2812 (ppp) REVERT: D 1406 GLU cc_start: 0.4580 (OUTLIER) cc_final: 0.3235 (pm20) REVERT: D 1474 ASP cc_start: 0.3403 (OUTLIER) cc_final: 0.2990 (p0) outliers start: 89 outliers final: 63 residues processed: 257 average time/residue: 0.3897 time to fit residues: 173.8306 Evaluate side-chains 239 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 172 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 860 MET Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 1065 SER Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1398 LEU Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1499 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 303 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN A 899 HIS ** A 968 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 GLN ** B 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN D 653 ASN ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1583 GLN ** E 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4337 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33556 Z= 0.285 Angle : 0.743 15.511 45324 Z= 0.378 Chirality : 0.045 0.321 5024 Planarity : 0.005 0.116 5796 Dihedral : 5.526 35.355 4394 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 26.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.48 % Allowed : 18.81 % Favored : 78.70 % 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: -1.78 (0.13), residues: 4022 helix: -0.31 (0.11), residues: 1896 sheet: -1.30 (0.30), residues: 280 loop : -2.10 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1538 HIS 0.009 0.001 HIS D 187 PHE 0.044 0.002 PHE D 976 TYR 0.024 0.002 TYR A 969 ARG 0.011 0.001 ARG D 931 *********************** 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 267 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 176 time to evaluate : 4.498 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: A 1 MET cc_start: 0.1140 (mmp) cc_final: 0.0781 (mmt) REVERT: A 40 MET cc_start: 0.4247 (tpp) cc_final: 0.4013 (tpp) REVERT: A 327 MET cc_start: -0.0701 (tmm) cc_final: -0.1883 (mtt) REVERT: A 595 MET cc_start: -0.2666 (mtt) cc_final: -0.2890 (mmt) REVERT: A 1406 GLU cc_start: 0.4691 (OUTLIER) cc_final: 0.3477 (pm20) REVERT: A 1474 ASP cc_start: 0.4135 (OUTLIER) cc_final: 0.3618 (p0) REVERT: B 145 MET cc_start: 0.5716 (tpt) cc_final: 0.5440 (mmm) REVERT: D 1 MET cc_start: 0.1545 (mmt) cc_final: 0.1304 (mmp) REVERT: D 327 MET cc_start: 0.0532 (pmm) cc_final: 0.0175 (ptm) REVERT: D 1406 GLU cc_start: 0.4513 (OUTLIER) cc_final: 0.2234 (pp20) REVERT: D 1474 ASP cc_start: 0.3980 (OUTLIER) cc_final: 0.3465 (p0) outliers start: 91 outliers final: 65 residues processed: 261 average time/residue: 0.3992 time to fit residues: 179.5597 Evaluate side-chains 240 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 171 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 899 HIS Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 860 MET Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1065 SER Chi-restraints excluded: chain D residue 1147 PHE Chi-restraints excluded: chain D residue 1148 GLU Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1398 LEU Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1499 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 350 optimal weight: 2.9990 chunk 369 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 359 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 324 optimal weight: 0.8980 chunk 339 optimal weight: 0.7980 chunk 358 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 968 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** B 104 HIS C 571 GLN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 556 ASN ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1048 HIS ** D1229 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4254 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33556 Z= 0.203 Angle : 0.724 14.538 45324 Z= 0.360 Chirality : 0.044 0.380 5024 Planarity : 0.005 0.122 5796 Dihedral : 5.416 33.714 4394 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.99 % Allowed : 19.55 % Favored : 78.45 % 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: -1.61 (0.13), residues: 4022 helix: -0.13 (0.11), residues: 1906 sheet: -1.33 (0.30), residues: 292 loop : -2.04 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D1538 HIS 0.020 0.001 HIS A 899 PHE 0.027 0.001 PHE A 787 TYR 0.017 0.001 TYR D1231 ARG 0.011 0.000 ARG D1088 *********************** 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 252 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 179 time to evaluate : 4.079 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: A 1 MET cc_start: 0.1073 (mmp) cc_final: 0.0824 (mmt) REVERT: A 327 MET cc_start: -0.1169 (tmm) cc_final: -0.2496 (mtt) REVERT: A 802 MET cc_start: 0.4898 (mmt) cc_final: 0.4689 (mmt) REVERT: A 1406 GLU cc_start: 0.4410 (OUTLIER) cc_final: 0.2243 (pm20) REVERT: A 1474 ASP cc_start: 0.4195 (OUTLIER) cc_final: 0.3665 (p0) REVERT: A 1549 MET cc_start: 0.4675 (mmm) cc_final: 0.4329 (mmm) REVERT: B 145 MET cc_start: 0.5732 (tpt) cc_final: 0.5499 (mmm) REVERT: D 364 MET cc_start: 0.4133 (mpp) cc_final: 0.3754 (mpp) REVERT: D 680 MET cc_start: 0.3177 (ppp) cc_final: 0.2901 (ppp) REVERT: D 1406 GLU cc_start: 0.4412 (OUTLIER) cc_final: 0.2249 (pp20) REVERT: D 1474 ASP cc_start: 0.3931 (OUTLIER) cc_final: 0.3443 (p0) REVERT: D 1549 MET cc_start: 0.4485 (mmm) cc_final: 0.4209 (mmm) outliers start: 73 outliers final: 56 residues processed: 246 average time/residue: 0.4203 time to fit residues: 178.7478 Evaluate side-chains 236 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 176 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1396 LEU Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 860 MET Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1065 SER Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1396 LEU Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1499 LEU Chi-restraints excluded: chain D residue 1639 VAL Chi-restraints excluded: chain F residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 235 optimal weight: 8.9990 chunk 379 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 180 optimal weight: 2.9990 chunk 264 optimal weight: 30.0000 chunk 398 optimal weight: 7.9990 chunk 366 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 245 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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** ** 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 556 ASN D 605 ASN ** D 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1229 ASN ** 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** E 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4401 moved from start: 0.4755 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= 0.328 Angle : 0.785 12.525 45324 Z= 0.400 Chirality : 0.046 0.399 5024 Planarity : 0.006 0.125 5796 Dihedral : 5.636 35.620 4394 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 30.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 2.08 % Allowed : 19.44 % Favored : 78.48 % 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: -1.88 (0.13), residues: 4022 helix: -0.49 (0.11), residues: 1912 sheet: -1.37 (0.30), residues: 292 loop : -2.03 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D1538 HIS 0.017 0.001 HIS A 968 PHE 0.024 0.002 PHE A 976 TYR 0.025 0.002 TYR A 972 ARG 0.009 0.001 ARG D 931 ********************** 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 253 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 177 time to evaluate : 3.946 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: A 327 MET cc_start: -0.0880 (tmm) cc_final: -0.2206 (mtt) REVERT: A 1406 GLU cc_start: 0.4695 (OUTLIER) cc_final: 0.2352 (pm20) REVERT: A 1474 ASP cc_start: 0.4355 (OUTLIER) cc_final: 0.3708 (p0) REVERT: A 1549 MET cc_start: 0.4754 (mmm) cc_final: 0.4495 (mmm) REVERT: B 145 MET cc_start: 0.5598 (tpt) cc_final: 0.5341 (mmm) REVERT: D 680 MET cc_start: 0.3265 (ppp) cc_final: 0.2995 (ppp) REVERT: D 943 MET cc_start: 0.1524 (ptm) cc_final: 0.1184 (ptm) REVERT: D 1406 GLU cc_start: 0.4515 (OUTLIER) cc_final: 0.2258 (pp20) REVERT: D 1474 ASP cc_start: 0.4185 (OUTLIER) cc_final: 0.3605 (p0) REVERT: D 1549 MET cc_start: 0.4684 (mmm) cc_final: 0.4364 (mmm) outliers start: 76 outliers final: 63 residues processed: 248 average time/residue: 0.4175 time to fit residues: 178.0571 Evaluate side-chains 241 residues out of total 3662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 174 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 192 LYS Chi-restraints excluded: chain A residue 242 PHE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 711 HIS Chi-restraints excluded: chain A residue 971 HIS Chi-restraints excluded: chain A residue 1065 SER Chi-restraints excluded: chain A residue 1147 PHE Chi-restraints excluded: chain A residue 1196 LEU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1281 HIS Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1291 TYR Chi-restraints excluded: chain A residue 1328 TYR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1406 GLU Chi-restraints excluded: chain A residue 1474 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 101 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 187 HIS Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 711 HIS Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 860 MET Chi-restraints excluded: chain D residue 971 HIS Chi-restraints excluded: chain D residue 978 THR Chi-restraints excluded: chain D residue 983 ILE Chi-restraints excluded: chain D residue 1065 SER Chi-restraints excluded: chain D residue 1147 PHE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1270 LEU Chi-restraints excluded: chain D residue 1281 HIS Chi-restraints excluded: chain D residue 1290 VAL Chi-restraints excluded: chain D residue 1291 TYR Chi-restraints excluded: chain D residue 1298 GLU Chi-restraints excluded: chain D residue 1328 TYR Chi-restraints excluded: chain D residue 1353 ILE Chi-restraints excluded: chain D residue 1406 GLU Chi-restraints excluded: chain D residue 1474 ASP Chi-restraints excluded: chain D residue 1490 THR Chi-restraints excluded: chain D residue 1498 ILE Chi-restraints excluded: chain D residue 1499 LEU Chi-restraints excluded: chain D residue 1639 VAL Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 681 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 252 optimal weight: 20.0000 chunk 338 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 292 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 326 optimal weight: 0.8980 chunk 40 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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** ** A 968 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** ** D1229 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.071880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.046462 restraints weight = 226075.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.047116 restraints weight = 159056.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.047479 restraints weight = 128280.125| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33556 Z= 0.185 Angle : 0.738 14.973 45324 Z= 0.365 Chirality : 0.044 0.376 5024 Planarity : 0.005 0.112 5796 Dihedral : 5.410 32.092 4394 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.56 % Allowed : 20.10 % Favored : 78.35 % 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: -1.62 (0.13), residues: 4022 helix: -0.11 (0.11), residues: 1914 sheet: -1.69 (0.30), residues: 302 loop : -2.01 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D1538 HIS 0.008 0.001 HIS A 968 PHE 0.031 0.001 PHE A 787 TYR 0.022 0.001 TYR C 720 ARG 0.007 0.001 ARG D 931 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7531.57 seconds wall clock time: 137 minutes 58.55 seconds (8278.55 seconds total)