Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 15 23:15:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/07_2023/6s8f_10120_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/07_2023/6s8f_10120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/07_2023/6s8f_10120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/07_2023/6s8f_10120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/07_2023/6s8f_10120_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/07_2023/6s8f_10120_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 21440 2.51 5 N 6016 2.21 5 O 6104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 971": "NH1" <-> "NH2" Residue "F ARG 1083": "NH1" <-> "NH2" Residue "F PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1334": "NH1" <-> "NH2" Residue "F ARG 1401": "NH1" <-> "NH2" Residue "F PHE 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1454": "NH1" <-> "NH2" Residue "F TYR 1481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1910": "NH1" <-> "NH2" Residue "F ARG 2020": "NH1" <-> "NH2" Residue "F ARG 2165": "NH1" <-> "NH2" Residue "F ARG 2202": "NH1" <-> "NH2" Residue "F ARG 2424": "NH1" <-> "NH2" Residue "F ARG 2427": "NH1" <-> "NH2" Residue "F ARG 2472": "NH1" <-> "NH2" Residue "F ARG 2495": "NH1" <-> "NH2" Residue "F ARG 2558": "NH1" <-> "NH2" Residue "H ARG 971": "NH1" <-> "NH2" Residue "H ARG 1083": "NH1" <-> "NH2" Residue "H PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1334": "NH1" <-> "NH2" Residue "H ARG 1401": "NH1" <-> "NH2" Residue "H PHE 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1454": "NH1" <-> "NH2" Residue "H TYR 1481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1910": "NH1" <-> "NH2" Residue "H ARG 2020": "NH1" <-> "NH2" Residue "H ARG 2165": "NH1" <-> "NH2" Residue "H ARG 2202": "NH1" <-> "NH2" Residue "H ARG 2424": "NH1" <-> "NH2" Residue "H ARG 2427": "NH1" <-> "NH2" Residue "H ARG 2472": "NH1" <-> "NH2" Residue "H ARG 2495": "NH1" <-> "NH2" Residue "H ARG 2558": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 33664 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 16800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2571, 16800 Classifications: {'peptide': 2571} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 1276} Link IDs: {'CIS': 3, 'PTRANS': 56, 'TRANS': 2511} Chain breaks: 23 Unresolved non-hydrogen bonds: 3216 Unresolved non-hydrogen angles: 4422 Unresolved non-hydrogen dihedrals: 2087 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 7, 'ASN:plan1': 42, 'TYR:plan': 11, 'UNK:plan-1': 806, 'ASP:plan': 53, 'PHE:plan': 15, 'GLU:plan': 76, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 1750 Chain: "H" Number of atoms: 16800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2571, 16800 Classifications: {'peptide': 2571} Incomplete info: {'backbone_only': 13, 'truncation_to_alanine': 1276} Link IDs: {'CIS': 3, 'PTRANS': 56, 'TRANS': 2511} Chain breaks: 23 Unresolved non-hydrogen bonds: 3216 Unresolved non-hydrogen angles: 4422 Unresolved non-hydrogen dihedrals: 2087 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 7, 'ASN:plan1': 42, 'TYR:plan': 11, 'UNK:plan-1': 806, 'ASP:plan': 53, 'PHE:plan': 15, 'GLU:plan': 76, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 1750 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.83, per 1000 atoms: 0.50 Number of scatterers: 33664 At special positions: 0 Unit cell: (107.415, 213.745, 201.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 6 15.00 Mg 2 11.99 O 6104 8.00 N 6016 7.00 C 21440 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: 14.76 Conformation dependent library (CDL) restraints added in 4.3 seconds 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 272 helices and 4 sheets defined 87.3% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.49 Creating SS restraints... Processing helix chain 'F' and resid 10 through 17 removed outlier: 4.587A pdb=" N UNK F 14 " --> pdb=" O UNK F 10 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N UNK F 15 " --> pdb=" O UNK F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 34 Processing helix chain 'F' and resid 45 through 69 Processing helix chain 'F' and resid 77 through 96 removed outlier: 3.993A pdb=" N UNK F 88 " --> pdb=" O UNK F 84 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N UNK F 89 " --> pdb=" O UNK F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 116 Processing helix chain 'F' and resid 131 through 146 removed outlier: 3.846A pdb=" N UNK F 140 " --> pdb=" O UNK F 136 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N UNK F 141 " --> pdb=" O UNK F 137 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N UNK F 142 " --> pdb=" O UNK F 138 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N UNK F 143 " --> pdb=" O UNK F 139 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N UNK F 144 " --> pdb=" O UNK F 140 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N UNK F 145 " --> pdb=" O UNK F 141 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N UNK F 146 " --> pdb=" O UNK F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 171 Processing helix chain 'F' and resid 177 through 192 removed outlier: 4.099A pdb=" N UNK F 181 " --> pdb=" O UNK F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 225 Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'F' and resid 241 through 249 Processing helix chain 'F' and resid 257 through 264 Processing helix chain 'F' and resid 281 through 292 removed outlier: 3.621A pdb=" N UNK F 285 " --> pdb=" O UNK F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 303 Processing helix chain 'F' and resid 310 through 318 Processing helix chain 'F' and resid 323 through 331 Processing helix chain 'F' and resid 335 through 344 removed outlier: 3.852A pdb=" N UNK F 341 " --> pdb=" O UNK F 337 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N UNK F 344 " --> pdb=" O UNK F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 376 removed outlier: 4.142A pdb=" N UNK F 367 " --> pdb=" O UNK F 363 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N UNK F 368 " --> pdb=" O UNK F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 430 removed outlier: 4.555A pdb=" N UNK F 427 " --> pdb=" O UNK F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 459 removed outlier: 3.570A pdb=" N UNK F 451 " --> pdb=" O UNK F 447 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK F 452 " --> pdb=" O UNK F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 488 Processing helix chain 'F' and resid 512 through 533 removed outlier: 3.897A pdb=" N UNK F 515 " --> pdb=" O UNK F 512 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N UNK F 516 " --> pdb=" O UNK F 513 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N UNK F 517 " --> pdb=" O UNK F 514 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N UNK F 518 " --> pdb=" O UNK F 515 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N UNK F 519 " --> pdb=" O UNK F 516 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N UNK F 528 " --> pdb=" O UNK F 525 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N UNK F 529 " --> pdb=" O UNK F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 572 removed outlier: 3.963A pdb=" N UNK F 569 " --> pdb=" O UNK F 565 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N UNK F 570 " --> pdb=" O UNK F 566 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N UNK F 571 " --> pdb=" O UNK F 567 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N UNK F 572 " --> pdb=" O UNK F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 589 removed outlier: 4.475A pdb=" N UNK F 585 " --> pdb=" O UNK F 581 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N UNK F 586 " --> pdb=" O UNK F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 607 Processing helix chain 'F' and resid 613 through 620 Processing helix chain 'F' and resid 627 through 638 Processing helix chain 'F' and resid 648 through 656 Processing helix chain 'F' and resid 667 through 677 removed outlier: 3.743A pdb=" N UNK F 671 " --> pdb=" O UNK F 667 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 685 No H-bonds generated for 'chain 'F' and resid 682 through 685' Processing helix chain 'F' and resid 687 through 694 Processing helix chain 'F' and resid 713 through 718 Processing helix chain 'F' and resid 748 through 759 removed outlier: 4.290A pdb=" N UNK F 753 " --> pdb=" O UNK F 749 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N UNK F 759 " --> pdb=" O UNK F 755 " (cutoff:3.500A) Processing helix chain 'F' and resid 773 through 788 removed outlier: 3.781A pdb=" N UNK F 783 " --> pdb=" O UNK F 779 " (cutoff:3.500A) Processing helix chain 'F' and resid 799 through 808 Processing helix chain 'F' and resid 821 through 835 removed outlier: 3.604A pdb=" N UNK F 834 " --> pdb=" O UNK F 830 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N UNK F 835 " --> pdb=" O UNK F 831 " (cutoff:3.500A) Processing helix chain 'F' and resid 840 through 849 Processing helix chain 'F' and resid 862 through 866 Processing helix chain 'F' and resid 884 through 898 removed outlier: 3.928A pdb=" N UNK F 894 " --> pdb=" O UNK F 890 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N UNK F 895 " --> pdb=" O UNK F 891 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N UNK F 896 " --> pdb=" O UNK F 892 " (cutoff:3.500A) Processing helix chain 'F' and resid 904 through 917 removed outlier: 4.707A pdb=" N UNK F 909 " --> pdb=" O UNK F 905 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N UNK F 910 " --> pdb=" O UNK F 906 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N UNK F 911 " --> pdb=" O UNK F 907 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N UNK F 912 " --> pdb=" O UNK F 908 " (cutoff:3.500A) Processing helix chain 'F' and resid 927 through 942 removed outlier: 3.625A pdb=" N UNK F 931 " --> pdb=" O UNK F 927 " (cutoff:3.500A) Processing helix chain 'F' and resid 949 through 963 Processing helix chain 'F' and resid 972 through 978 Processing helix chain 'F' and resid 983 through 989 removed outlier: 4.326A pdb=" N LEU F 988 " --> pdb=" O CYS F 984 " (cutoff:3.500A) Processing helix chain 'F' and resid 994 through 1000 removed outlier: 3.601A pdb=" N ASN F 998 " --> pdb=" O ILE F 994 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER F 999 " --> pdb=" O ASN F 995 " (cutoff:3.500A) Processing helix chain 'F' and resid 1003 through 1015 Processing helix chain 'F' and resid 1025 through 1032 removed outlier: 3.510A pdb=" N ILE F1030 " --> pdb=" O PRO F1026 " (cutoff:3.500A) Processing helix chain 'F' and resid 1038 through 1046 removed outlier: 3.555A pdb=" N VAL F1046 " --> pdb=" O MET F1042 " (cutoff:3.500A) Processing helix chain 'F' and resid 1057 through 1071 Processing helix chain 'F' and resid 1085 through 1089 Processing helix chain 'F' and resid 1134 through 1140 removed outlier: 3.638A pdb=" N SER F1139 " --> pdb=" O PHE F1135 " (cutoff:3.500A) Processing helix chain 'F' and resid 1153 through 1159 Processing helix chain 'F' and resid 1164 through 1170 Processing helix chain 'F' and resid 1172 through 1178 removed outlier: 3.929A pdb=" N ILE F1176 " --> pdb=" O TYR F1172 " (cutoff:3.500A) Proline residue: F1177 - end of helix No H-bonds generated for 'chain 'F' and resid 1172 through 1178' Processing helix chain 'F' and resid 1201 through 1207 Processing helix chain 'F' and resid 1209 through 1218 Processing helix chain 'F' and resid 1227 through 1235 Processing helix chain 'F' and resid 1244 through 1252 removed outlier: 4.055A pdb=" N SER F1252 " --> pdb=" O ASN F1248 " (cutoff:3.500A) Processing helix chain 'F' and resid 1267 through 1275 removed outlier: 3.663A pdb=" N VAL F1270 " --> pdb=" O ALA F1267 " (cutoff:3.500A) Processing helix chain 'F' and resid 1281 through 1297 Processing helix chain 'F' and resid 1301 through 1317 removed outlier: 3.579A pdb=" N LYS F1312 " --> pdb=" O ALA F1308 " (cutoff:3.500A) Processing helix chain 'F' and resid 1325 through 1341 removed outlier: 3.842A pdb=" N ARG F1334 " --> pdb=" O PHE F1330 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS F1337 " --> pdb=" O ILE F1333 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE F1338 " --> pdb=" O ARG F1334 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N LEU F1339 " --> pdb=" O LEU F1335 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE F1340 " --> pdb=" O SER F1336 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP F1341 " --> pdb=" O LYS F1337 " (cutoff:3.500A) Processing helix chain 'F' and resid 1345 through 1361 removed outlier: 3.991A pdb=" N ILE F1351 " --> pdb=" O GLU F1347 " (cutoff:3.500A) Processing helix chain 'F' and resid 1367 through 1382 Proline residue: F1371 - end of helix removed outlier: 3.964A pdb=" N CYS F1375 " --> pdb=" O ASN F1372 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE F1377 " --> pdb=" O PHE F1374 " (cutoff:3.500A) Processing helix chain 'F' and resid 1389 through 1399 removed outlier: 3.547A pdb=" N LEU F1397 " --> pdb=" O GLN F1393 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU F1398 " --> pdb=" O ALA F1394 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU F1399 " --> pdb=" O ILE F1395 " (cutoff:3.500A) Processing helix chain 'F' and resid 1406 through 1416 Processing helix chain 'F' and resid 1423 through 1427 removed outlier: 4.157A pdb=" N TYR F1426 " --> pdb=" O ASP F1423 " (cutoff:3.500A) Processing helix chain 'F' and resid 1430 through 1433 No H-bonds generated for 'chain 'F' and resid 1430 through 1433' Processing helix chain 'F' and resid 1439 through 1451 removed outlier: 4.867A pdb=" N TYR F1451 " --> pdb=" O LEU F1447 " (cutoff:3.500A) Processing helix chain 'F' and resid 1457 through 1460 No H-bonds generated for 'chain 'F' and resid 1457 through 1460' Processing helix chain 'F' and resid 1485 through 1505 removed outlier: 4.791A pdb=" N ARG F1495 " --> pdb=" O ALA F1491 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ARG F1496 " --> pdb=" O ALA F1492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F1503 " --> pdb=" O GLN F1499 " (cutoff:3.500A) Processing helix chain 'F' and resid 1514 through 1523 Processing helix chain 'F' and resid 1530 through 1540 removed outlier: 3.665A pdb=" N GLN F1534 " --> pdb=" O HIS F1530 " (cutoff:3.500A) Processing helix chain 'F' and resid 1543 through 1547 removed outlier: 3.829A pdb=" N ASP F1547 " --> pdb=" O GLU F1544 " (cutoff:3.500A) Processing helix chain 'F' and resid 1551 through 1564 Processing helix chain 'F' and resid 1577 through 1580 No H-bonds generated for 'chain 'F' and resid 1577 through 1580' Processing helix chain 'F' and resid 1590 through 1596 Processing helix chain 'F' and resid 1612 through 1614 No H-bonds generated for 'chain 'F' and resid 1612 through 1614' Processing helix chain 'F' and resid 1623 through 1638 removed outlier: 3.658A pdb=" N GLN F1637 " --> pdb=" O SER F1633 " (cutoff:3.500A) Processing helix chain 'F' and resid 1644 through 1653 Proline residue: F1650 - end of helix Processing helix chain 'F' and resid 1658 through 1672 removed outlier: 4.498A pdb=" N THR F1664 " --> pdb=" O GLU F1660 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASP F1665 " --> pdb=" O LEU F1661 " (cutoff:3.500A) Processing helix chain 'F' and resid 1675 through 1688 removed outlier: 4.299A pdb=" N ASN F1680 " --> pdb=" O LYS F1676 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F1684 " --> pdb=" O ASN F1680 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE F1685 " --> pdb=" O TRP F1681 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN F1688 " --> pdb=" O ARG F1684 " (cutoff:3.500A) Processing helix chain 'F' and resid 1691 through 1693 No H-bonds generated for 'chain 'F' and resid 1691 through 1693' Processing helix chain 'F' and resid 1698 through 1717 Processing helix chain 'F' and resid 1721 through 1729 removed outlier: 3.747A pdb=" N ARG F1725 " --> pdb=" O ARG F1721 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER F1729 " --> pdb=" O ARG F1725 " (cutoff:3.500A) Processing helix chain 'F' and resid 1732 through 1741 removed outlier: 3.922A pdb=" N LEU F1740 " --> pdb=" O CYS F1736 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS F1741 " --> pdb=" O GLN F1737 " (cutoff:3.500A) Processing helix chain 'F' and resid 1745 through 1755 Processing helix chain 'F' and resid 1760 through 1762 No H-bonds generated for 'chain 'F' and resid 1760 through 1762' Processing helix chain 'F' and resid 1765 through 1773 removed outlier: 4.142A pdb=" N LYS F1770 " --> pdb=" O ASN F1766 " (cutoff:3.500A) Processing helix chain 'F' and resid 1781 through 1783 No H-bonds generated for 'chain 'F' and resid 1781 through 1783' Processing helix chain 'F' and resid 1790 through 1799 Processing helix chain 'F' and resid 1804 through 1821 removed outlier: 5.704A pdb=" N THR F1820 " --> pdb=" O ASP F1816 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR F1821 " --> pdb=" O ALA F1817 " (cutoff:3.500A) Processing helix chain 'F' and resid 1825 through 1837 removed outlier: 3.586A pdb=" N SER F1829 " --> pdb=" O GLU F1826 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE F1831 " --> pdb=" O GLU F1828 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS F1832 " --> pdb=" O SER F1829 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU F1835 " --> pdb=" O LYS F1832 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP F1836 " --> pdb=" O ALA F1833 " (cutoff:3.500A) Processing helix chain 'F' and resid 1840 through 1844 Processing helix chain 'F' and resid 1856 through 1863 Processing helix chain 'F' and resid 1878 through 1886 Processing helix chain 'F' and resid 1895 through 1908 Processing helix chain 'F' and resid 1916 through 1935 removed outlier: 5.003A pdb=" N ILE F1935 " --> pdb=" O LYS F1931 " (cutoff:3.500A) Processing helix chain 'F' and resid 1942 through 1958 removed outlier: 3.867A pdb=" N GLU F1955 " --> pdb=" O LYS F1951 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F1957 " --> pdb=" O ASP F1953 " (cutoff:3.500A) Processing helix chain 'F' and resid 1962 through 1985 removed outlier: 5.167A pdb=" N THR F1967 " --> pdb=" O TYR F1963 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR F1968 " --> pdb=" O ASP F1964 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASP F1985 " --> pdb=" O ARG F1981 " (cutoff:3.500A) Processing helix chain 'F' and resid 1988 through 2011 removed outlier: 3.663A pdb=" N LYS F1992 " --> pdb=" O VAL F1988 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR F1993 " --> pdb=" O LYS F1989 " (cutoff:3.500A) Processing helix chain 'F' and resid 2015 through 2033 removed outlier: 3.699A pdb=" N ARG F2020 " --> pdb=" O GLN F2016 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN F2021 " --> pdb=" O ASP F2017 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN F2031 " --> pdb=" O LYS F2027 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE F2032 " --> pdb=" O THR F2028 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA F2033 " --> pdb=" O VAL F2029 " (cutoff:3.500A) Processing helix chain 'F' and resid 2039 through 2059 Processing helix chain 'F' and resid 2065 through 2079 Processing helix chain 'F' and resid 2082 through 2084 No H-bonds generated for 'chain 'F' and resid 2082 through 2084' Processing helix chain 'F' and resid 2108 through 2111 No H-bonds generated for 'chain 'F' and resid 2108 through 2111' Processing helix chain 'F' and resid 2117 through 2123 Processing helix chain 'F' and resid 2138 through 2158 removed outlier: 3.578A pdb=" N PHE F2142 " --> pdb=" O CYS F2138 " (cutoff:3.500A) Processing helix chain 'F' and resid 2162 through 2179 removed outlier: 3.575A pdb=" N HIS F2167 " --> pdb=" O GLU F2163 " (cutoff:3.500A) Processing helix chain 'F' and resid 2201 through 2236 Processing helix chain 'F' and resid 2245 through 2256 removed outlier: 3.945A pdb=" N LYS F2249 " --> pdb=" O ASP F2245 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY F2252 " --> pdb=" O ASP F2248 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N PHE F2255 " --> pdb=" O CYS F2251 " (cutoff:3.500A) Processing helix chain 'F' and resid 2261 through 2265 Processing helix chain 'F' and resid 2267 through 2270 No H-bonds generated for 'chain 'F' and resid 2267 through 2270' Processing helix chain 'F' and resid 2276 through 2281 removed outlier: 3.560A pdb=" N LEU F2280 " --> pdb=" O TRP F2277 " (cutoff:3.500A) Proline residue: F2281 - end of helix Processing helix chain 'F' and resid 2284 through 2287 No H-bonds generated for 'chain 'F' and resid 2284 through 2287' Processing helix chain 'F' and resid 2299 through 2311 removed outlier: 3.558A pdb=" N ARG F2307 " --> pdb=" O LEU F2303 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR F2310 " --> pdb=" O LYS F2306 " (cutoff:3.500A) Processing helix chain 'F' and resid 2317 through 2326 Processing helix chain 'F' and resid 2334 through 2351 removed outlier: 3.580A pdb=" N LYS F2339 " --> pdb=" O ASN F2335 " (cutoff:3.500A) Processing helix chain 'F' and resid 2358 through 2361 No H-bonds generated for 'chain 'F' and resid 2358 through 2361' Processing helix chain 'F' and resid 2363 through 2376 Processing helix chain 'F' and resid 2396 through 2401 Processing helix chain 'F' and resid 2473 through 2490 removed outlier: 4.172A pdb=" N ASN F2490 " --> pdb=" O LYS F2486 " (cutoff:3.500A) Processing helix chain 'F' and resid 2492 through 2495 No H-bonds generated for 'chain 'F' and resid 2492 through 2495' Processing helix chain 'F' and resid 2525 through 2532 Processing helix chain 'F' and resid 2540 through 2549 removed outlier: 3.577A pdb=" N ARG F2544 " --> pdb=" O PHE F2540 " (cutoff:3.500A) Processing helix chain 'F' and resid 2555 through 2568 removed outlier: 4.346A pdb=" N GLU F2568 " --> pdb=" O LYS F2564 " (cutoff:3.500A) Processing helix chain 'F' and resid 2573 through 2580 removed outlier: 4.196A pdb=" N SER F2580 " --> pdb=" O PHE F2577 " (cutoff:3.500A) Processing helix chain 'F' and resid 2584 through 2607 removed outlier: 4.459A pdb=" N GLU F2589 " --> pdb=" O LEU F2585 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS F2596 " --> pdb=" O LYS F2592 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F2604 " --> pdb=" O ALA F2600 " (cutoff:3.500A) Processing helix chain 'F' and resid 2638 through 2640 No H-bonds generated for 'chain 'F' and resid 2638 through 2640' Processing helix chain 'F' and resid 2654 through 2659 Processing helix chain 'F' and resid 2669 through 2682 removed outlier: 3.761A pdb=" N VAL F2679 " --> pdb=" O ARG F2675 " (cutoff:3.500A) Processing helix chain 'F' and resid 2685 through 2693 removed outlier: 4.395A pdb=" N ILE F2693 " --> pdb=" O CYS F2689 " (cutoff:3.500A) Processing helix chain 'F' and resid 2708 through 2716 Processing helix chain 'F' and resid 2737 through 2753 removed outlier: 3.699A pdb=" N MET F2753 " --> pdb=" O GLU F2749 " (cutoff:3.500A) Processing helix chain 'F' and resid 2759 through 2770 removed outlier: 3.918A pdb=" N GLN F2764 " --> pdb=" O GLU F2760 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F2766 " --> pdb=" O SER F2762 " (cutoff:3.500A) Processing helix chain 'F' and resid 2773 through 2776 No H-bonds generated for 'chain 'F' and resid 2773 through 2776' Processing helix chain 'H' and resid 10 through 17 removed outlier: 4.628A pdb=" N UNK H 14 " --> pdb=" O UNK H 10 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N UNK H 15 " --> pdb=" O UNK H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 34 Processing helix chain 'H' and resid 45 through 69 Processing helix chain 'H' and resid 77 through 96 removed outlier: 3.970A pdb=" N UNK H 88 " --> pdb=" O UNK H 84 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK H 89 " --> pdb=" O UNK H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 131 through 146 removed outlier: 3.924A pdb=" N UNK H 140 " --> pdb=" O UNK H 136 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N UNK H 141 " --> pdb=" O UNK H 137 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N UNK H 142 " --> pdb=" O UNK H 138 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N UNK H 143 " --> pdb=" O UNK H 139 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N UNK H 144 " --> pdb=" O UNK H 140 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N UNK H 145 " --> pdb=" O UNK H 141 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N UNK H 146 " --> pdb=" O UNK H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 171 Processing helix chain 'H' and resid 175 through 192 removed outlier: 4.164A pdb=" N UNK H 180 " --> pdb=" O UNK H 176 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N UNK H 181 " --> pdb=" O UNK H 177 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N UNK H 183 " --> pdb=" O UNK H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 225 Processing helix chain 'H' and resid 231 through 233 No H-bonds generated for 'chain 'H' and resid 231 through 233' Processing helix chain 'H' and resid 241 through 249 Processing helix chain 'H' and resid 255 through 264 removed outlier: 3.502A pdb=" N UNK H 258 " --> pdb=" O UNK H 255 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N UNK H 263 " --> pdb=" O UNK H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 292 removed outlier: 3.617A pdb=" N UNK H 285 " --> pdb=" O UNK H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 303 Processing helix chain 'H' and resid 310 through 318 Processing helix chain 'H' and resid 323 through 331 Processing helix chain 'H' and resid 335 through 344 removed outlier: 3.865A pdb=" N UNK H 341 " --> pdb=" O UNK H 337 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N UNK H 344 " --> pdb=" O UNK H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 376 removed outlier: 4.135A pdb=" N UNK H 367 " --> pdb=" O UNK H 363 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N UNK H 368 " --> pdb=" O UNK H 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 423 through 430 removed outlier: 4.564A pdb=" N UNK H 427 " --> pdb=" O UNK H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 459 removed outlier: 3.580A pdb=" N UNK H 451 " --> pdb=" O UNK H 447 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N UNK H 452 " --> pdb=" O UNK H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 488 Processing helix chain 'H' and resid 512 through 533 removed outlier: 3.880A pdb=" N UNK H 515 " --> pdb=" O UNK H 512 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N UNK H 516 " --> pdb=" O UNK H 513 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N UNK H 517 " --> pdb=" O UNK H 514 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N UNK H 518 " --> pdb=" O UNK H 515 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N UNK H 519 " --> pdb=" O UNK H 516 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N UNK H 528 " --> pdb=" O UNK H 525 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N UNK H 529 " --> pdb=" O UNK H 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 572 removed outlier: 3.908A pdb=" N UNK H 569 " --> pdb=" O UNK H 565 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N UNK H 570 " --> pdb=" O UNK H 566 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N UNK H 571 " --> pdb=" O UNK H 567 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N UNK H 572 " --> pdb=" O UNK H 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 589 removed outlier: 4.492A pdb=" N UNK H 585 " --> pdb=" O UNK H 581 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N UNK H 586 " --> pdb=" O UNK H 582 " (cutoff:3.500A) Processing helix chain 'H' and resid 603 through 607 Processing helix chain 'H' and resid 613 through 620 Processing helix chain 'H' and resid 627 through 638 Processing helix chain 'H' and resid 648 through 656 Processing helix chain 'H' and resid 667 through 677 removed outlier: 3.733A pdb=" N UNK H 671 " --> pdb=" O UNK H 667 " (cutoff:3.500A) Processing helix chain 'H' and resid 682 through 685 No H-bonds generated for 'chain 'H' and resid 682 through 685' Processing helix chain 'H' and resid 687 through 694 Processing helix chain 'H' and resid 713 through 718 Processing helix chain 'H' and resid 748 through 759 removed outlier: 4.286A pdb=" N UNK H 753 " --> pdb=" O UNK H 749 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N UNK H 759 " --> pdb=" O UNK H 755 " (cutoff:3.500A) Processing helix chain 'H' and resid 773 through 788 removed outlier: 3.780A pdb=" N UNK H 783 " --> pdb=" O UNK H 779 " (cutoff:3.500A) Processing helix chain 'H' and resid 799 through 808 Processing helix chain 'H' and resid 821 through 835 removed outlier: 3.586A pdb=" N UNK H 834 " --> pdb=" O UNK H 830 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK H 835 " --> pdb=" O UNK H 831 " (cutoff:3.500A) Processing helix chain 'H' and resid 840 through 849 Processing helix chain 'H' and resid 862 through 866 Processing helix chain 'H' and resid 884 through 898 removed outlier: 3.917A pdb=" N UNK H 894 " --> pdb=" O UNK H 890 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N UNK H 895 " --> pdb=" O UNK H 891 " (cutoff:3.500A) Processing helix chain 'H' and resid 904 through 917 removed outlier: 4.673A pdb=" N UNK H 909 " --> pdb=" O UNK H 905 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK H 910 " --> pdb=" O UNK H 906 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N UNK H 911 " --> pdb=" O UNK H 907 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N UNK H 912 " --> pdb=" O UNK H 908 " (cutoff:3.500A) Processing helix chain 'H' and resid 927 through 942 removed outlier: 3.628A pdb=" N UNK H 931 " --> pdb=" O UNK H 927 " (cutoff:3.500A) Processing helix chain 'H' and resid 949 through 963 Processing helix chain 'H' and resid 972 through 978 Processing helix chain 'H' and resid 983 through 989 removed outlier: 4.325A pdb=" N LEU H 988 " --> pdb=" O CYS H 984 " (cutoff:3.500A) Processing helix chain 'H' and resid 994 through 1000 removed outlier: 3.608A pdb=" N ASN H 998 " --> pdb=" O ILE H 994 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER H 999 " --> pdb=" O ASN H 995 " (cutoff:3.500A) Processing helix chain 'H' and resid 1003 through 1015 Processing helix chain 'H' and resid 1025 through 1032 removed outlier: 3.508A pdb=" N ILE H1030 " --> pdb=" O PRO H1026 " (cutoff:3.500A) Processing helix chain 'H' and resid 1038 through 1046 removed outlier: 3.557A pdb=" N VAL H1046 " --> pdb=" O MET H1042 " (cutoff:3.500A) Processing helix chain 'H' and resid 1057 through 1071 Processing helix chain 'H' and resid 1085 through 1089 Processing helix chain 'H' and resid 1134 through 1140 removed outlier: 3.636A pdb=" N SER H1139 " --> pdb=" O PHE H1135 " (cutoff:3.500A) Processing helix chain 'H' and resid 1153 through 1159 Processing helix chain 'H' and resid 1164 through 1170 Processing helix chain 'H' and resid 1172 through 1178 removed outlier: 3.932A pdb=" N ILE H1176 " --> pdb=" O TYR H1172 " (cutoff:3.500A) Proline residue: H1177 - end of helix No H-bonds generated for 'chain 'H' and resid 1172 through 1178' Processing helix chain 'H' and resid 1201 through 1207 Processing helix chain 'H' and resid 1209 through 1218 Processing helix chain 'H' and resid 1227 through 1235 Processing helix chain 'H' and resid 1244 through 1252 removed outlier: 4.085A pdb=" N SER H1252 " --> pdb=" O ASN H1248 " (cutoff:3.500A) Processing helix chain 'H' and resid 1267 through 1274 removed outlier: 3.637A pdb=" N VAL H1270 " --> pdb=" O ALA H1267 " (cutoff:3.500A) Processing helix chain 'H' and resid 1281 through 1297 Processing helix chain 'H' and resid 1301 through 1317 removed outlier: 3.580A pdb=" N LYS H1312 " --> pdb=" O ALA H1308 " (cutoff:3.500A) Processing helix chain 'H' and resid 1325 through 1341 removed outlier: 3.835A pdb=" N ARG H1334 " --> pdb=" O PHE H1330 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LYS H1337 " --> pdb=" O ILE H1333 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE H1338 " --> pdb=" O ARG H1334 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LEU H1339 " --> pdb=" O LEU H1335 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE H1340 " --> pdb=" O SER H1336 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ASP H1341 " --> pdb=" O LYS H1337 " (cutoff:3.500A) Processing helix chain 'H' and resid 1345 through 1361 removed outlier: 3.987A pdb=" N ILE H1351 " --> pdb=" O GLU H1347 " (cutoff:3.500A) Processing helix chain 'H' and resid 1367 through 1382 Proline residue: H1371 - end of helix removed outlier: 3.961A pdb=" N CYS H1375 " --> pdb=" O ASN H1372 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE H1377 " --> pdb=" O PHE H1374 " (cutoff:3.500A) Processing helix chain 'H' and resid 1389 through 1399 removed outlier: 3.569A pdb=" N LEU H1397 " --> pdb=" O GLN H1393 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU H1398 " --> pdb=" O ALA H1394 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU H1399 " --> pdb=" O ILE H1395 " (cutoff:3.500A) Processing helix chain 'H' and resid 1406 through 1416 Processing helix chain 'H' and resid 1423 through 1427 removed outlier: 4.157A pdb=" N TYR H1426 " --> pdb=" O ASP H1423 " (cutoff:3.500A) Processing helix chain 'H' and resid 1430 through 1433 No H-bonds generated for 'chain 'H' and resid 1430 through 1433' Processing helix chain 'H' and resid 1439 through 1451 removed outlier: 4.872A pdb=" N TYR H1451 " --> pdb=" O LEU H1447 " (cutoff:3.500A) Processing helix chain 'H' and resid 1457 through 1460 No H-bonds generated for 'chain 'H' and resid 1457 through 1460' Processing helix chain 'H' and resid 1485 through 1505 removed outlier: 4.790A pdb=" N ARG H1495 " --> pdb=" O ALA H1491 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG H1496 " --> pdb=" O ALA H1492 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN H1503 " --> pdb=" O GLN H1499 " (cutoff:3.500A) Processing helix chain 'H' and resid 1514 through 1523 Processing helix chain 'H' and resid 1530 through 1540 removed outlier: 3.646A pdb=" N GLN H1534 " --> pdb=" O HIS H1530 " (cutoff:3.500A) Processing helix chain 'H' and resid 1543 through 1547 removed outlier: 3.825A pdb=" N ASP H1547 " --> pdb=" O GLU H1544 " (cutoff:3.500A) Processing helix chain 'H' and resid 1551 through 1564 Processing helix chain 'H' and resid 1577 through 1580 No H-bonds generated for 'chain 'H' and resid 1577 through 1580' Processing helix chain 'H' and resid 1590 through 1596 Processing helix chain 'H' and resid 1612 through 1614 No H-bonds generated for 'chain 'H' and resid 1612 through 1614' Processing helix chain 'H' and resid 1623 through 1638 removed outlier: 3.645A pdb=" N GLN H1637 " --> pdb=" O SER H1633 " (cutoff:3.500A) Processing helix chain 'H' and resid 1644 through 1653 Proline residue: H1650 - end of helix Processing helix chain 'H' and resid 1658 through 1672 removed outlier: 4.494A pdb=" N THR H1664 " --> pdb=" O GLU H1660 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP H1665 " --> pdb=" O LEU H1661 " (cutoff:3.500A) Processing helix chain 'H' and resid 1675 through 1688 removed outlier: 4.304A pdb=" N ASN H1680 " --> pdb=" O LYS H1676 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG H1684 " --> pdb=" O ASN H1680 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ILE H1685 " --> pdb=" O TRP H1681 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN H1688 " --> pdb=" O ARG H1684 " (cutoff:3.500A) Processing helix chain 'H' and resid 1691 through 1693 No H-bonds generated for 'chain 'H' and resid 1691 through 1693' Processing helix chain 'H' and resid 1698 through 1717 Processing helix chain 'H' and resid 1723 through 1729 removed outlier: 4.542A pdb=" N SER H1729 " --> pdb=" O ARG H1725 " (cutoff:3.500A) Processing helix chain 'H' and resid 1732 through 1741 removed outlier: 3.920A pdb=" N LEU H1740 " --> pdb=" O CYS H1736 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS H1741 " --> pdb=" O GLN H1737 " (cutoff:3.500A) Processing helix chain 'H' and resid 1745 through 1755 Processing helix chain 'H' and resid 1760 through 1762 No H-bonds generated for 'chain 'H' and resid 1760 through 1762' Processing helix chain 'H' and resid 1765 through 1773 removed outlier: 4.130A pdb=" N LYS H1770 " --> pdb=" O ASN H1766 " (cutoff:3.500A) Processing helix chain 'H' and resid 1781 through 1783 No H-bonds generated for 'chain 'H' and resid 1781 through 1783' Processing helix chain 'H' and resid 1790 through 1799 Processing helix chain 'H' and resid 1804 through 1821 removed outlier: 5.697A pdb=" N THR H1820 " --> pdb=" O ASP H1816 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR H1821 " --> pdb=" O ALA H1817 " (cutoff:3.500A) Processing helix chain 'H' and resid 1825 through 1837 removed outlier: 3.573A pdb=" N SER H1829 " --> pdb=" O GLU H1826 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE H1831 " --> pdb=" O GLU H1828 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS H1832 " --> pdb=" O SER H1829 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU H1835 " --> pdb=" O LYS H1832 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP H1836 " --> pdb=" O ALA H1833 " (cutoff:3.500A) Processing helix chain 'H' and resid 1840 through 1844 Processing helix chain 'H' and resid 1856 through 1863 Processing helix chain 'H' and resid 1878 through 1886 Processing helix chain 'H' and resid 1895 through 1908 Processing helix chain 'H' and resid 1916 through 1935 removed outlier: 5.004A pdb=" N ILE H1935 " --> pdb=" O LYS H1931 " (cutoff:3.500A) Processing helix chain 'H' and resid 1942 through 1958 removed outlier: 3.869A pdb=" N GLU H1955 " --> pdb=" O LYS H1951 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU H1957 " --> pdb=" O ASP H1953 " (cutoff:3.500A) Processing helix chain 'H' and resid 1962 through 1985 removed outlier: 5.169A pdb=" N THR H1967 " --> pdb=" O TYR H1963 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR H1968 " --> pdb=" O ASP H1964 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP H1985 " --> pdb=" O ARG H1981 " (cutoff:3.500A) Processing helix chain 'H' and resid 1988 through 2011 removed outlier: 3.655A pdb=" N LYS H1992 " --> pdb=" O VAL H1988 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR H1993 " --> pdb=" O LYS H1989 " (cutoff:3.500A) Processing helix chain 'H' and resid 2015 through 2033 removed outlier: 3.703A pdb=" N ARG H2020 " --> pdb=" O GLN H2016 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN H2021 " --> pdb=" O ASP H2017 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN H2031 " --> pdb=" O LYS H2027 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE H2032 " --> pdb=" O THR H2028 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA H2033 " --> pdb=" O VAL H2029 " (cutoff:3.500A) Processing helix chain 'H' and resid 2039 through 2059 Processing helix chain 'H' and resid 2065 through 2079 Processing helix chain 'H' and resid 2082 through 2084 No H-bonds generated for 'chain 'H' and resid 2082 through 2084' Processing helix chain 'H' and resid 2108 through 2111 No H-bonds generated for 'chain 'H' and resid 2108 through 2111' Processing helix chain 'H' and resid 2117 through 2123 Processing helix chain 'H' and resid 2138 through 2158 removed outlier: 3.578A pdb=" N PHE H2142 " --> pdb=" O CYS H2138 " (cutoff:3.500A) Processing helix chain 'H' and resid 2162 through 2179 removed outlier: 3.552A pdb=" N HIS H2167 " --> pdb=" O GLU H2163 " (cutoff:3.500A) Processing helix chain 'H' and resid 2201 through 2236 Processing helix chain 'H' and resid 2245 through 2256 removed outlier: 3.943A pdb=" N LYS H2249 " --> pdb=" O ASP H2245 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY H2252 " --> pdb=" O ASP H2248 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE H2255 " --> pdb=" O CYS H2251 " (cutoff:3.500A) Processing helix chain 'H' and resid 2261 through 2265 Processing helix chain 'H' and resid 2267 through 2270 No H-bonds generated for 'chain 'H' and resid 2267 through 2270' Processing helix chain 'H' and resid 2276 through 2281 removed outlier: 3.560A pdb=" N LEU H2280 " --> pdb=" O TRP H2277 " (cutoff:3.500A) Proline residue: H2281 - end of helix Processing helix chain 'H' and resid 2284 through 2287 No H-bonds generated for 'chain 'H' and resid 2284 through 2287' Processing helix chain 'H' and resid 2299 through 2311 removed outlier: 3.549A pdb=" N ARG H2307 " --> pdb=" O LEU H2303 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR H2310 " --> pdb=" O LYS H2306 " (cutoff:3.500A) Processing helix chain 'H' and resid 2317 through 2324 Processing helix chain 'H' and resid 2334 through 2351 removed outlier: 3.578A pdb=" N LYS H2339 " --> pdb=" O ASN H2335 " (cutoff:3.500A) Processing helix chain 'H' and resid 2358 through 2361 No H-bonds generated for 'chain 'H' and resid 2358 through 2361' Processing helix chain 'H' and resid 2363 through 2376 Processing helix chain 'H' and resid 2396 through 2401 Processing helix chain 'H' and resid 2473 through 2490 removed outlier: 4.173A pdb=" N ASN H2490 " --> pdb=" O LYS H2486 " (cutoff:3.500A) Processing helix chain 'H' and resid 2492 through 2495 No H-bonds generated for 'chain 'H' and resid 2492 through 2495' Processing helix chain 'H' and resid 2525 through 2532 Processing helix chain 'H' and resid 2540 through 2549 removed outlier: 3.577A pdb=" N ARG H2544 " --> pdb=" O PHE H2540 " (cutoff:3.500A) Processing helix chain 'H' and resid 2555 through 2568 removed outlier: 4.345A pdb=" N GLU H2568 " --> pdb=" O LYS H2564 " (cutoff:3.500A) Processing helix chain 'H' and resid 2573 through 2580 removed outlier: 4.195A pdb=" N SER H2580 " --> pdb=" O PHE H2577 " (cutoff:3.500A) Processing helix chain 'H' and resid 2584 through 2607 removed outlier: 4.459A pdb=" N GLU H2589 " --> pdb=" O LEU H2585 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS H2596 " --> pdb=" O LYS H2592 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL H2604 " --> pdb=" O ALA H2600 " (cutoff:3.500A) Processing helix chain 'H' and resid 2638 through 2640 No H-bonds generated for 'chain 'H' and resid 2638 through 2640' Processing helix chain 'H' and resid 2654 through 2659 Processing helix chain 'H' and resid 2669 through 2682 removed outlier: 3.761A pdb=" N VAL H2679 " --> pdb=" O ARG H2675 " (cutoff:3.500A) Processing helix chain 'H' and resid 2685 through 2693 removed outlier: 4.395A pdb=" N ILE H2693 " --> pdb=" O CYS H2689 " (cutoff:3.500A) Processing helix chain 'H' and resid 2708 through 2716 Processing helix chain 'H' and resid 2737 through 2753 removed outlier: 3.699A pdb=" N MET H2753 " --> pdb=" O GLU H2749 " (cutoff:3.500A) Processing helix chain 'H' and resid 2759 through 2770 removed outlier: 3.918A pdb=" N GLN H2764 " --> pdb=" O GLU H2760 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU H2766 " --> pdb=" O SER H2762 " (cutoff:3.500A) Processing helix chain 'H' and resid 2773 through 2776 No H-bonds generated for 'chain 'H' and resid 2773 through 2776' Processing sheet with id= A, first strand: chain 'F' and resid 2387 through 2389 Processing sheet with id= B, first strand: chain 'F' and resid 2451 through 2453 Processing sheet with id= C, first strand: chain 'H' and resid 2387 through 2389 Processing sheet with id= D, first strand: chain 'H' and resid 2451 through 2453 1762 hydrogen bonds defined for protein. 5016 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.69 Time building geometry restraints manager: 15.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11087 1.34 - 1.46: 5723 1.46 - 1.57: 17194 1.57 - 1.69: 10 1.69 - 1.81: 150 Bond restraints: 34164 Sorted by residual: bond pdb=" O3A ANP H2801 " pdb=" PB ANP H2801 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.48e+01 bond pdb=" O3A ANP F2801 " pdb=" PB ANP F2801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" N3B ANP F2801 " pdb=" PG ANP F2801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" N3B ANP H2801 " pdb=" PG ANP H2801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O5' ANP H2801 " pdb=" PA ANP H2801 " ideal model delta sigma weight residual 1.655 1.573 0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 34159 not shown) Histogram of bond angle deviations from ideal: 78.16 - 94.73: 2 94.73 - 111.31: 14449 111.31 - 127.88: 32122 127.88 - 144.46: 263 144.46 - 161.03: 4 Bond angle restraints: 46840 Sorted by residual: angle pdb=" O ARG F2355 " pdb=" C ARG F2355 " pdb=" N GLY F2356 " ideal model delta sigma weight residual 122.59 78.16 44.43 1.33e+00 5.65e-01 1.12e+03 angle pdb=" O ARG H2355 " pdb=" C ARG H2355 " pdb=" N GLY H2356 " ideal model delta sigma weight residual 122.59 80.90 41.69 1.33e+00 5.65e-01 9.83e+02 angle pdb=" CA ARG F2355 " pdb=" C ARG F2355 " pdb=" N GLY F2356 " ideal model delta sigma weight residual 116.84 159.94 -43.10 1.71e+00 3.42e-01 6.35e+02 angle pdb=" CA ARG H2355 " pdb=" C ARG H2355 " pdb=" N GLY H2356 " ideal model delta sigma weight residual 116.84 156.90 -40.06 1.71e+00 3.42e-01 5.49e+02 angle pdb=" C ARG F2355 " pdb=" N GLY F2356 " pdb=" CA GLY F2356 " ideal model delta sigma weight residual 121.07 161.03 -39.96 1.79e+00 3.12e-01 4.98e+02 ... (remaining 46835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 19000 15.79 - 31.57: 972 31.57 - 47.36: 220 47.36 - 63.15: 22 63.15 - 78.93: 32 Dihedral angle restraints: 20246 sinusoidal: 5050 harmonic: 15196 Sorted by residual: dihedral pdb=" CA LYS F2380 " pdb=" C LYS F2380 " pdb=" N PHE F2381 " pdb=" CA PHE F2381 " ideal model delta harmonic sigma weight residual 180.00 106.16 73.84 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA LYS H2380 " pdb=" C LYS H2380 " pdb=" N PHE H2381 " pdb=" CA PHE H2381 " ideal model delta harmonic sigma weight residual 180.00 106.18 73.82 0 5.00e+00 4.00e-02 2.18e+02 dihedral pdb=" CA VAL H1786 " pdb=" C VAL H1786 " pdb=" N PRO H1787 " pdb=" CA PRO H1787 " ideal model delta harmonic sigma weight residual 180.00 -117.62 -62.38 0 5.00e+00 4.00e-02 1.56e+02 ... (remaining 20243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4889 0.073 - 0.147: 847 0.147 - 0.220: 90 0.220 - 0.294: 8 0.294 - 0.367: 10 Chirality restraints: 5844 Sorted by residual: chirality pdb=" CB ILE H2449 " pdb=" CA ILE H2449 " pdb=" CG1 ILE H2449 " pdb=" CG2 ILE H2449 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE F2449 " pdb=" CA ILE F2449 " pdb=" CG1 ILE F2449 " pdb=" CG2 ILE F2449 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE H2644 " pdb=" CA ILE H2644 " pdb=" CG1 ILE H2644 " pdb=" CG2 ILE H2644 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 5841 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H1786 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO H1787 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO H1787 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO H1787 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F1786 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO F1787 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO F1787 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO F1787 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG H2355 " -0.029 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C ARG H2355 " 0.070 2.00e-02 2.50e+03 pdb=" O ARG H2355 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY H2356 " -0.028 2.00e-02 2.50e+03 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 119 2.47 - 3.08: 22452 3.08 - 3.68: 53579 3.68 - 4.29: 69378 4.29 - 4.90: 107967 Nonbonded interactions: 253495 Sorted by model distance: nonbonded pdb=" NH2 ARG H1717 " pdb=" OD1 ASP H2579 " model vdw 1.859 2.520 nonbonded pdb=" NH2 ARG F1717 " pdb=" OD1 ASP F2579 " model vdw 1.902 2.520 nonbonded pdb=" O2G ANP H2801 " pdb="MG MG H2802 " model vdw 2.100 2.170 nonbonded pdb=" O2G ANP F2801 " pdb="MG MG F2802 " model vdw 2.100 2.170 nonbonded pdb=" O1A ANP F2801 " pdb="MG MG F2802 " model vdw 2.102 2.170 ... (remaining 253490 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 'F' selection = chain 'H' } 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.820 Check model and map are aligned: 0.500 Set scattering table: 0.340 Process input model: 83.430 Find NCS groups from input model: 1.910 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.007 0.148 34164 Z= 0.450 Angle : 1.263 44.429 46840 Z= 0.681 Chirality : 0.058 0.367 5844 Planarity : 0.007 0.104 6088 Dihedral : 11.676 78.932 10274 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.58 % Favored : 90.30 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.64 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.11), residues: 3506 helix: -2.53 (0.08), residues: 2130 sheet: -3.38 (0.57), residues: 66 loop : -3.33 (0.14), residues: 1310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 3.313 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 outliers start: 18 outliers final: 0 residues processed: 181 average time/residue: 0.4427 time to fit residues: 134.8265 Evaluate side-chains 110 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 3.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1027 GLN ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1384 ASN ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1707 ASN ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1795 ASN ** F1798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1977 ASN ** F1987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2135 HIS ** F2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2489 GLN F2490 ASN F2526 HIS ** F2572 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1027 GLN ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1384 ASN ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1707 ASN ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1795 ASN ** H1798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1977 ASN H1987 ASN ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2489 GLN H2490 ASN H2526 HIS ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.043 0.515 34164 Z= 2.806 Angle : 2.982 38.228 46840 Z= 1.558 Chirality : 0.106 0.884 5844 Planarity : 0.020 0.154 6088 Dihedral : 11.959 68.828 5338 Min Nonbonded Distance : 1.500 Molprobity Statistics. All-atom Clashscore : 145.63 Ramachandran Plot: Outliers : 3.85 % Allowed : 26.18 % Favored : 69.97 % Rotamer Outliers : 15.97 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 2.73 % 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: -6.44 (0.10), residues: 3506 helix: -4.13 (0.07), residues: 2112 sheet: -4.11 (0.41), residues: 78 loop : -4.27 (0.15), residues: 1316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 82 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 361 outliers final: 209 residues processed: 427 average time/residue: 0.3925 time to fit residues: 289.7944 Evaluate side-chains 289 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 80 time to evaluate : 3.339 Switching outliers to nearest non-outliers outliers start: 209 outliers final: 2 residues processed: 209 average time/residue: 0.3391 time to fit residues: 132.4465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1624 ASN ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1624 ASN ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2001 GLN ** H2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.8773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.478 34164 Z= 2.749 Angle : 2.909 38.193 46840 Z= 1.507 Chirality : 0.104 0.824 5844 Planarity : 0.019 0.156 6088 Dihedral : 13.011 70.998 5338 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 169.13 Ramachandran Plot: Outliers : 3.05 % Allowed : 42.18 % Favored : 54.76 % Rotamer Outliers : 24.56 % Cbeta Deviations : 0.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 3.96 % 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: -7.37 (0.09), residues: 3506 helix: -4.67 (0.06), residues: 2066 sheet: -4.09 (0.47), residues: 56 loop : -5.13 (0.13), residues: 1384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 555 poor density : 78 time to evaluate : 3.606 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 outliers start: 555 outliers final: 389 residues processed: 620 average time/residue: 0.4222 time to fit residues: 436.4340 Evaluate side-chains 468 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 79 time to evaluate : 3.387 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 389 outliers final: 6 residues processed: 389 average time/residue: 0.3461 time to fit residues: 244.1523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2001 GLN ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2738 ASN ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1597 ASN ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2738 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.9593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.515 34164 Z= 2.745 Angle : 2.906 38.842 46840 Z= 1.499 Chirality : 0.106 0.864 5844 Planarity : 0.019 0.157 6088 Dihedral : 13.306 73.687 5338 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 177.64 Ramachandran Plot: Outliers : 2.94 % Allowed : 47.46 % Favored : 49.60 % Rotamer Outliers : 25.97 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 4.34 % 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: -7.70 (0.08), residues: 3506 helix: -4.81 (0.05), residues: 2082 sheet: -4.07 (0.54), residues: 56 loop : -5.50 (0.12), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 587 poor density : 78 time to evaluate : 3.273 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 outliers start: 587 outliers final: 400 residues processed: 648 average time/residue: 0.4449 time to fit residues: 479.7420 Evaluate side-chains 481 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 81 time to evaluate : 3.397 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 400 outliers final: 5 residues processed: 400 average time/residue: 0.3555 time to fit residues: 257.2795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1597 ASN ** F1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1707 ASN ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2080 ASN ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1688 GLN H1707 ASN ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H2080 ASN ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2473 GLN ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 1.0112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.520 34164 Z= 2.737 Angle : 2.893 38.127 46840 Z= 1.493 Chirality : 0.107 0.869 5844 Planarity : 0.019 0.158 6088 Dihedral : 13.477 78.903 5338 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 183.07 Ramachandran Plot: Outliers : 2.68 % Allowed : 49.34 % Favored : 47.97 % Rotamer Outliers : 24.34 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 4.84 % 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: -7.81 (0.08), residues: 3506 helix: -4.85 (0.05), residues: 2078 sheet: -3.80 (0.66), residues: 52 loop : -5.65 (0.12), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 550 poor density : 80 time to evaluate : 3.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 550 outliers final: 373 residues processed: 619 average time/residue: 0.4590 time to fit residues: 469.5653 Evaluate side-chains 451 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 373 poor density : 78 time to evaluate : 3.556 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 373 outliers final: 6 residues processed: 373 average time/residue: 0.3602 time to fit residues: 241.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1624 ASN ** F1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2496 ASN ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1624 ASN ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1788 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2473 GLN ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2496 ASN ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 1.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.522 34164 Z= 2.735 Angle : 2.912 39.162 46840 Z= 1.500 Chirality : 0.108 0.867 5844 Planarity : 0.019 0.156 6088 Dihedral : 13.598 79.422 5338 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 186.26 Ramachandran Plot: Outliers : 2.60 % Allowed : 50.91 % Favored : 46.49 % Rotamer Outliers : 22.04 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 5.02 % 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: -7.87 (0.08), residues: 3506 helix: -4.89 (0.05), residues: 2028 sheet: -4.01 (0.62), residues: 52 loop : -5.70 (0.11), residues: 1426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 498 poor density : 80 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 498 outliers final: 335 residues processed: 560 average time/residue: 0.4514 time to fit residues: 416.0160 Evaluate side-chains 415 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 80 time to evaluate : 3.257 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 335 outliers final: 4 residues processed: 335 average time/residue: 0.3508 time to fit residues: 213.4401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1534 GLN ** F1624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2496 ASN ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1973 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2496 ASN ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 1.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.517 34164 Z= 2.731 Angle : 2.906 40.331 46840 Z= 1.500 Chirality : 0.109 0.857 5844 Planarity : 0.019 0.165 6088 Dihedral : 13.706 80.472 5338 Min Nonbonded Distance : 1.610 Molprobity Statistics. All-atom Clashscore : 186.22 Ramachandran Plot: Outliers : 2.45 % Allowed : 52.31 % Favored : 45.24 % Rotamer Outliers : 16.77 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.18 % Twisted General : 4.96 % 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: -7.95 (0.08), residues: 3506 helix: -4.92 (0.05), residues: 2046 sheet: -4.11 (0.57), residues: 52 loop : -5.79 (0.11), residues: 1408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 79 time to evaluate : 3.406 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 outliers start: 379 outliers final: 232 residues processed: 451 average time/residue: 0.4488 time to fit residues: 335.1990 Evaluate side-chains 310 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 78 time to evaluate : 3.449 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 232 outliers final: 6 residues processed: 232 average time/residue: 0.3893 time to fit residues: 163.0158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2496 ASN ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2473 GLN ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2496 ASN ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 1.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.519 34164 Z= 2.731 Angle : 2.909 39.120 46840 Z= 1.504 Chirality : 0.109 0.859 5844 Planarity : 0.019 0.181 6088 Dihedral : 13.796 81.258 5338 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 187.61 Ramachandran Plot: Outliers : 2.31 % Allowed : 52.42 % Favored : 45.27 % Rotamer Outliers : 12.96 % Cbeta Deviations : 0.96 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 5.31 % 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: -7.96 (0.07), residues: 3506 helix: -4.92 (0.05), residues: 2042 sheet: -4.30 (0.53), residues: 52 loop : -5.81 (0.11), residues: 1412 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 78 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 293 outliers final: 189 residues processed: 353 average time/residue: 0.4466 time to fit residues: 265.3029 Evaluate side-chains 267 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 78 time to evaluate : 3.351 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 6 residues processed: 189 average time/residue: 0.3787 time to fit residues: 130.2083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 8.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1624 ASN ** F1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2496 ASN ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2496 ASN ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 1.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.523 34164 Z= 2.741 Angle : 2.916 39.743 46840 Z= 1.508 Chirality : 0.111 0.863 5844 Planarity : 0.019 0.184 6088 Dihedral : 13.849 81.543 5338 Min Nonbonded Distance : 1.575 Molprobity Statistics. All-atom Clashscore : 186.49 Ramachandran Plot: Outliers : 2.42 % Allowed : 53.19 % Favored : 44.38 % Rotamer Outliers : 8.45 % Cbeta Deviations : 1.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 5.40 % 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: -7.96 (0.08), residues: 3506 helix: -4.88 (0.05), residues: 2032 sheet: -4.21 (0.56), residues: 52 loop : -5.87 (0.11), residues: 1422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 78 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 114 residues processed: 263 average time/residue: 0.4684 time to fit residues: 209.1556 Evaluate side-chains 193 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 79 time to evaluate : 3.885 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 5 residues processed: 114 average time/residue: 0.4188 time to fit residues: 93.0673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1688 GLN ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2496 ASN ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 1.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.526 34164 Z= 2.742 Angle : 2.929 40.436 46840 Z= 1.513 Chirality : 0.111 0.953 5844 Planarity : 0.019 0.168 6088 Dihedral : 13.903 81.710 5338 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 186.99 Ramachandran Plot: Outliers : 2.42 % Allowed : 52.94 % Favored : 44.64 % Rotamer Outliers : 5.35 % Cbeta Deviations : 1.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.91 % Twisted General : 5.55 % 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: -7.98 (0.08), residues: 3506 helix: -4.93 (0.05), residues: 2026 sheet: -4.20 (0.60), residues: 52 loop : -5.83 (0.11), residues: 1428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 78 time to evaluate : 3.599 Fit side-chains revert: symmetry clash outliers start: 121 outliers final: 66 residues processed: 182 average time/residue: 0.4519 time to fit residues: 140.8006 Evaluate side-chains 145 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 79 time to evaluate : 3.440 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 2 residues processed: 66 average time/residue: 0.3699 time to fit residues: 48.0969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 0 random chunks: chunk None optimal weight: 7.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1624 ASN ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2076 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2496 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2617 ASN ** 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 = 0.3106 r_free = 0.3106 target = 0.038045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.027811 restraints weight = 476544.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.028246 restraints weight = 304492.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.028562 restraints weight = 224032.460| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 1.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.042 0.522 34164 Z= 2.746 Angle : 2.930 40.401 46840 Z= 1.512 Chirality : 0.111 0.874 5844 Planarity : 0.019 0.171 6088 Dihedral : 13.953 81.930 5338 Min Nonbonded Distance : 1.488 Molprobity Statistics. All-atom Clashscore : 187.52 Ramachandran Plot: Outliers : 2.42 % Allowed : 53.14 % Favored : 44.44 % Rotamer Outliers : 3.89 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 5.75 % 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: -7.96 (0.08), residues: 3506 helix: -4.91 (0.05), residues: 2002 sheet: -4.18 (0.61), residues: 52 loop : -5.84 (0.11), residues: 1452 =============================================================================== Job complete usr+sys time: 13551.23 seconds wall clock time: 243 minutes 0.02 seconds (14580.02 seconds total)