Starting phenix.real_space_refine on Sat Dec 16 02:48:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/12_2023/6s8f_10120_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/12_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_10120/12_2023/6s8f_10120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/12_2023/6s8f_10120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/12_2023/6s8f_10120_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8f_10120/12_2023/6s8f_10120_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 18.02, per 1000 atoms: 0.54 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: 13.22 Conformation dependent library (CDL) restraints added in 5.2 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: 16.99 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: 14.56 Time building geometry restraints manager: 14.34 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: 19040 15.79 - 31.57: 976 31.57 - 47.36: 228 47.36 - 63.15: 24 63.15 - 78.93: 34 Dihedral angle restraints: 20302 sinusoidal: 5106 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 20299 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: 2.290 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: 0.040 Extract box with map and model: 13.210 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 90.110 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.840 ------------------------------------------------------------------------------- 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 : 11.787 78.932 10330 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 % Allowed : 11.06 % Favored : 88.14 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP H2108 HIS 0.012 0.003 HIS H1475 PHE 0.042 0.004 PHE H1780 TYR 0.023 0.002 TYR F1411 ARG 0.008 0.001 ARG F2613 *********************** 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 : 3.565 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: 0.5052 time to fit residues: 155.0850 Evaluate side-chains 110 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 5.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.2834 ------------------------------------------------------------------------------- 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** ** F1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** 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** ** 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 ** F2575 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** ** H1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1694 HIS ** 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** ** H1887 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** ** H2367 GLN ** 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.043 0.512 34164 Z= 2.798 Angle : 3.002 37.609 46840 Z= 1.568 Chirality : 0.105 0.872 5844 Planarity : 0.020 0.156 6088 Dihedral : 12.360 68.860 5394 Min Nonbonded Distance : 1.446 Molprobity Statistics. All-atom Clashscore : 149.23 Ramachandran Plot: Outliers : 4.14 % Allowed : 26.10 % Favored : 69.77 % Rotamer: Outliers : 16.99 % Allowed : 16.37 % Favored : 66.64 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 2.90 % 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: -6.50 (0.10), residues: 3506 helix: -4.14 (0.06), residues: 2108 sheet: -4.22 (0.39), residues: 78 loop : -4.37 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.011 TRP F2254 HIS 0.037 0.009 HIS F2230 PHE 0.114 0.012 PHE F1808 TYR 0.085 0.009 TYR H2005 ARG 0.033 0.004 ARG H2389 *********************** 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 466 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 82 time to evaluate : 3.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 384 outliers final: 224 residues processed: 450 average time/residue: 0.4084 time to fit residues: 318.1937 Evaluate side-chains 304 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 80 time to evaluate : 3.242 Switching outliers to nearest non-outliers outliers start: 224 outliers final: 2 residues processed: 224 average time/residue: 0.3544 time to fit residues: 147.2492 ------------------------------------------------------------------------------- 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** ** F1384 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 ** 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** ** 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** ** H1384 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 ** 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.8716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.511 34164 Z= 2.751 Angle : 2.907 38.321 46840 Z= 1.505 Chirality : 0.105 0.863 5844 Planarity : 0.019 0.162 6088 Dihedral : 13.136 71.300 5394 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 168.18 Ramachandran Plot: Outliers : 3.05 % Allowed : 42.36 % Favored : 54.59 % Rotamer: Outliers : 24.87 % Allowed : 21.37 % Favored : 53.76 % Cbeta Deviations : 0.70 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 4.08 % 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: -7.39 (0.09), residues: 3506 helix: -4.68 (0.06), residues: 2112 sheet: -4.16 (0.45), residues: 56 loop : -5.12 (0.13), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.011 TRP F2226 HIS 0.035 0.008 HIS F1476 PHE 0.079 0.011 PHE F1808 TYR 0.060 0.009 TYR H2594 ARG 0.034 0.004 ARG H2165 *********************** 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 640 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 562 poor density : 78 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 562 outliers final: 395 residues processed: 628 average time/residue: 0.4223 time to fit residues: 443.2599 Evaluate side-chains 474 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 79 time to evaluate : 3.400 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 395 outliers final: 6 residues processed: 395 average time/residue: 0.3556 time to fit residues: 256.3917 ------------------------------------------------------------------------------- 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** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1384 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** F2044 GLN ** 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** ** F2434 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** ** F2617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2738 ASN ** 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** ** H1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1384 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** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2044 GLN ** 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** ** H2483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2738 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.9546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.530 34164 Z= 2.740 Angle : 2.909 38.835 46840 Z= 1.499 Chirality : 0.106 0.862 5844 Planarity : 0.019 0.157 6088 Dihedral : 13.431 73.660 5394 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 177.21 Ramachandran Plot: Outliers : 2.85 % Allowed : 47.75 % Favored : 49.40 % Rotamer: Outliers : 25.35 % Allowed : 27.83 % Favored : 46.81 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 4.55 % 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: -7.74 (0.08), residues: 3506 helix: -4.80 (0.05), residues: 2098 sheet: -3.90 (0.58), residues: 52 loop : -5.60 (0.12), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.010 TRP H2226 HIS 0.037 0.008 HIS F1476 PHE 0.071 0.011 PHE H1780 TYR 0.076 0.009 TYR F1481 ARG 0.034 0.003 ARG H2389 *********************** 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 651 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 573 poor density : 78 time to evaluate : 3.317 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: 573 outliers final: 397 residues processed: 634 average time/residue: 0.4322 time to fit residues: 458.4619 Evaluate side-chains 479 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 397 poor density : 82 time to evaluate : 3.725 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 397 outliers final: 5 residues processed: 397 average time/residue: 0.3947 time to fit residues: 286.8330 ------------------------------------------------------------------------------- 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** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1384 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 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** ** 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** ** F2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2468 ASN ** 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** ** 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** ** H1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1471 ASN ** 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** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** 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** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 1.0043 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= 2.738 Angle : 2.893 37.856 46840 Z= 1.493 Chirality : 0.107 0.868 5844 Planarity : 0.019 0.159 6088 Dihedral : 13.594 76.852 5394 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 182.73 Ramachandran Plot: Outliers : 2.45 % Allowed : 50.48 % Favored : 47.06 % Rotamer: Outliers : 24.42 % Allowed : 31.42 % Favored : 44.16 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 4.72 % 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: -7.83 (0.08), residues: 3506 helix: -4.84 (0.05), residues: 2106 sheet: -4.28 (0.61), residues: 40 loop : -5.67 (0.12), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.011 TRP H2226 HIS 0.036 0.008 HIS F1476 PHE 0.078 0.010 PHE F1374 TYR 0.077 0.009 TYR F1208 ARG 0.033 0.003 ARG H1496 *********************** 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 632 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 552 poor density : 80 time to evaluate : 4.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 552 outliers final: 368 residues processed: 622 average time/residue: 0.4489 time to fit residues: 460.4997 Evaluate side-chains 446 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 78 time to evaluate : 3.751 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 368 outliers final: 7 residues processed: 368 average time/residue: 0.3861 time to fit residues: 256.9200 ------------------------------------------------------------------------------- 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** ** F1384 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 ** 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** ** 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** ** F2341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2468 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** ** H1384 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** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** 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** ** H2298 GLN ** 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 1.0441 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= 2.734 Angle : 2.907 39.431 46840 Z= 1.497 Chirality : 0.107 0.863 5844 Planarity : 0.019 0.159 6088 Dihedral : 13.679 79.823 5394 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 184.74 Ramachandran Plot: Outliers : 2.51 % Allowed : 51.45 % Favored : 46.04 % Rotamer: Outliers : 22.04 % Allowed : 34.69 % Favored : 43.27 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % 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: -7.91 (0.08), residues: 3506 helix: -4.87 (0.05), residues: 2026 sheet: -3.94 (0.61), residues: 52 loop : -5.82 (0.11), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.011 TRP H1805 HIS 0.035 0.008 HIS F1476 PHE 0.071 0.010 PHE H1780 TYR 0.082 0.009 TYR F1208 ARG 0.039 0.003 ARG H1496 *********************** 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 577 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 498 poor density : 79 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 498 outliers final: 338 residues processed: 562 average time/residue: 0.4575 time to fit residues: 423.2273 Evaluate side-chains 418 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 80 time to evaluate : 3.393 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 338 outliers final: 5 residues processed: 338 average time/residue: 0.3700 time to fit residues: 224.5962 ------------------------------------------------------------------------------- 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** ** F1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1624 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** ** 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** ** F2298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2468 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** ** H1384 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** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** 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** ** H2298 GLN ** 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 1.0723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.518 34164 Z= 2.729 Angle : 2.902 40.271 46840 Z= 1.499 Chirality : 0.109 0.861 5844 Planarity : 0.019 0.156 6088 Dihedral : 13.786 80.262 5394 Min Nonbonded Distance : 1.617 Molprobity Statistics. All-atom Clashscore : 185.54 Ramachandran Plot: Outliers : 2.48 % Allowed : 51.97 % Favored : 45.55 % Rotamer: Outliers : 16.81 % Allowed : 38.67 % Favored : 44.51 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.18 % Twisted General : 4.67 % 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: -7.97 (0.08), residues: 3506 helix: -4.91 (0.05), residues: 2030 sheet: -4.09 (0.56), residues: 52 loop : -5.86 (0.11), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.011 TRP F1805 HIS 0.037 0.008 HIS F1476 PHE 0.072 0.010 PHE F1780 TYR 0.089 0.009 TYR H1208 ARG 0.032 0.003 ARG H1496 *********************** 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: 380 poor density : 78 time to evaluate : 3.652 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: 380 outliers final: 223 residues processed: 450 average time/residue: 0.4530 time to fit residues: 338.5969 Evaluate side-chains 301 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 78 time to evaluate : 3.217 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 5 residues processed: 223 average time/residue: 0.3629 time to fit residues: 148.0523 ------------------------------------------------------------------------------- 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** ** F1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** 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** ** 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** ** F2298 GLN ** 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** ** F2468 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** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1384 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 ** H1624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** 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** ** H2298 GLN ** 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** ** 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: 0.8706 moved from start: 1.0968 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= 2.729 Angle : 2.903 39.431 46840 Z= 1.501 Chirality : 0.110 0.888 5844 Planarity : 0.019 0.157 6088 Dihedral : 13.824 80.571 5394 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 186.53 Ramachandran Plot: Outliers : 2.51 % Allowed : 52.91 % Favored : 44.58 % Rotamer: Outliers : 12.88 % Allowed : 42.12 % Favored : 45.00 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.18 % Twisted General : 4.90 % 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: -8.00 (0.07), residues: 3506 helix: -4.90 (0.05), residues: 2024 sheet: -4.34 (0.52), residues: 52 loop : -5.93 (0.11), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.094 0.011 TRP H1805 HIS 0.037 0.009 HIS F1476 PHE 0.074 0.010 PHE H1780 TYR 0.077 0.009 TYR H1257 ARG 0.038 0.004 ARG F1496 *********************** 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 369 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 78 time to evaluate : 3.513 Fit side-chains revert: symmetry clash outliers start: 291 outliers final: 189 residues processed: 358 average time/residue: 0.4597 time to fit residues: 277.5429 Evaluate side-chains 267 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 78 time to evaluate : 3.562 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 5 residues processed: 189 average time/residue: 0.3873 time to fit residues: 135.2898 ------------------------------------------------------------------------------- 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** ** F1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1624 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** ** 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** ** F2298 GLN ** 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** ** F2468 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** ** H1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 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** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** 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** ** 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 ** 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: 0.8706 moved from start: 1.1175 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= 2.742 Angle : 2.912 40.055 46840 Z= 1.505 Chirality : 0.110 0.872 5844 Planarity : 0.019 0.157 6088 Dihedral : 13.859 81.158 5394 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 185.14 Ramachandran Plot: Outliers : 2.60 % Allowed : 53.19 % Favored : 44.21 % Rotamer: Outliers : 8.45 % Allowed : 45.40 % Favored : 46.15 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.27 % Twisted General : 5.05 % 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: -7.99 (0.07), residues: 3506 helix: -4.91 (0.05), residues: 2012 sheet: -4.65 (0.46), residues: 52 loop : -5.87 (0.11), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.122 0.011 TRP H1805 HIS 0.038 0.009 HIS F1476 PHE 0.070 0.010 PHE H1780 TYR 0.075 0.009 TYR F1208 ARG 0.034 0.004 ARG H1496 *********************** 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 : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 102 residues processed: 261 average time/residue: 0.4257 time to fit residues: 188.3654 Evaluate side-chains 180 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 78 time to evaluate : 3.206 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 2 residues processed: 102 average time/residue: 0.3430 time to fit residues: 68.3015 ------------------------------------------------------------------------------- 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** ** F1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1624 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** ** 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** ** F2298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2341 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** ** F2468 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** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 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** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** 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** ** H2298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2341 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** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 1.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.042 0.521 34164 Z= 2.746 Angle : 2.920 39.446 46840 Z= 1.511 Chirality : 0.110 0.868 5844 Planarity : 0.019 0.185 6088 Dihedral : 13.984 81.715 5394 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 186.71 Ramachandran Plot: Outliers : 2.62 % Allowed : 52.91 % Favored : 44.47 % Rotamer: Outliers : 5.09 % Allowed : 46.81 % Favored : 48.10 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.18 % Twisted General : 5.13 % 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: -8.04 (0.07), residues: 3506 helix: -4.93 (0.05), residues: 1998 sheet: -4.40 (0.53), residues: 52 loop : -5.94 (0.11), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.107 0.011 TRP H1805 HIS 0.039 0.009 HIS F1476 PHE 0.070 0.010 PHE H1780 TYR 0.111 0.009 TYR F1318 ARG 0.042 0.004 ARG H1496 ********************** 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 193 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 78 time to evaluate : 3.352 Fit side-chains revert: symmetry clash outliers start: 115 outliers final: 61 residues processed: 181 average time/residue: 0.4554 time to fit residues: 139.1925 Evaluate side-chains 140 residues out of total 3226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 79 time to evaluate : 3.493 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 2 residues processed: 61 average time/residue: 0.3772 time to fit residues: 44.7451 ------------------------------------------------------------------------------- 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: 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** ** F1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1534 GLN ** 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** ** F2001 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** ** F2298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2341 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** ** F2468 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** ** H1357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1860 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2012 ASN ** 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** ** H2298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H2341 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.038065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.027810 restraints weight = 478769.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.028255 restraints weight = 304315.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.028569 restraints weight = 221732.124| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 1.1511 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= 2.746 Angle : 2.924 39.633 46840 Z= 1.510 Chirality : 0.110 0.873 5844 Planarity : 0.019 0.171 6088 Dihedral : 14.040 81.542 5394 Min Nonbonded Distance : 1.498 Molprobity Statistics. All-atom Clashscore : 186.47 Ramachandran Plot: Outliers : 2.51 % Allowed : 53.08 % Favored : 44.41 % Rotamer: Outliers : 4.82 % Allowed : 46.77 % Favored : 48.41 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 5.16 % 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: -8.01 (0.07), residues: 3506 helix: -4.92 (0.05), residues: 1964 sheet: -4.43 (0.53), residues: 52 loop : -5.91 (0.10), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.011 TRP F2108 HIS 0.036 0.009 HIS F1476 PHE 0.072 0.010 PHE H1780 TYR 0.116 0.009 TYR H1318 ARG 0.042 0.004 ARG F1496 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13805.45 seconds wall clock time: 249 minutes 6.89 seconds (14946.89 seconds total)