Starting phenix.real_space_refine on Wed Jul 30 23:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hyp_0309/07_2025/6hyp_0309_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hyp_0309/07_2025/6hyp_0309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6hyp_0309/07_2025/6hyp_0309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hyp_0309/07_2025/6hyp_0309.map" model { file = "/net/cci-nas-00/data/ceres_data/6hyp_0309/07_2025/6hyp_0309_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hyp_0309/07_2025/6hyp_0309_neut.cif" } resolution = 4.4 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 10 5.16 5 C 7587 2.51 5 N 2390 2.21 5 O 2401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12392 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2272, 12338 Classifications: {'peptide': 2272} Incomplete info: {'truncation_to_alanine': 1766} Link IDs: {'PTRANS': 83, 'TRANS': 2188} Chain breaks: 22 Unresolved chain link angles: 64 Unresolved non-hydrogen bonds: 5829 Unresolved non-hydrogen angles: 7520 Unresolved non-hydrogen dihedrals: 4650 Unresolved non-hydrogen chiralities: 559 Planarities with less than four sites: {'GLN:plan1': 56, 'ARG:plan': 75, 'TYR:plan': 35, 'UNK:plan-1': 190, 'TRP:plan': 17, 'ASP:plan': 103, 'ASN:plan1': 98, 'PHE:plan': 80, 'GLU:plan': 132, 'HIS:plan': 32} Unresolved non-hydrogen planarities: 2958 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.18, per 1000 atoms: 0.74 Number of scatterers: 12392 At special positions: 0 Unit cell: (108.9, 170.5, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 4 15.00 O 2401 8.00 N 2390 7.00 C 7587 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 - 3.00 Amino acid : True - 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: 3.05 Conformation dependent library (CDL) restraints added in 2.1 seconds 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4348 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 11 sheets defined 50.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 removed outlier: 4.365A pdb=" N UNK A 24 " --> pdb=" O UNK A 20 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N UNK A 25 " --> pdb=" O UNK A 21 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N UNK A 26 " --> pdb=" O UNK A 22 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N UNK A 30 " --> pdb=" O UNK A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.747A pdb=" N UNK A 77 " --> pdb=" O UNK A 73 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N UNK A 78 " --> pdb=" O UNK A 74 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N UNK A 79 " --> pdb=" O UNK A 75 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N UNK A 82 " --> pdb=" O UNK A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.796A pdb=" N UNK A 90 " --> pdb=" O UNK A 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N UNK A 93 " --> pdb=" O UNK A 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N UNK A 94 " --> pdb=" O UNK A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 removed outlier: 3.599A pdb=" N UNK A 118 " --> pdb=" O UNK A 115 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N UNK A 119 " --> pdb=" O UNK A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.594A pdb=" N UNK A 127 " --> pdb=" O UNK A 123 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N UNK A 130 " --> pdb=" O UNK A 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N UNK A 132 " --> pdb=" O UNK A 128 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N UNK A 138 " --> pdb=" O UNK A 134 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N UNK A 139 " --> pdb=" O UNK A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 154 through 162 removed outlier: 4.033A pdb=" N UNK A 160 " --> pdb=" O UNK A 156 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK A 161 " --> pdb=" O UNK A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 removed outlier: 4.019A pdb=" N UNK A 170 " --> pdb=" O UNK A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.583A pdb=" N UNK A 177 " --> pdb=" O UNK A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 4.040A pdb=" N UNK A 190 " --> pdb=" O UNK A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 238 through 250 removed outlier: 3.581A pdb=" N GLU A 242 " --> pdb=" O PRO A 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 3.797A pdb=" N ASP A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.612A pdb=" N LYS A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 332 removed outlier: 3.661A pdb=" N ILE A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 removed outlier: 3.702A pdb=" N ALA A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 removed outlier: 4.240A pdb=" N ILE A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.864A pdb=" N LEU A 407 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.799A pdb=" N HIS A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 472 " --> pdb=" O HIS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 492 removed outlier: 3.600A pdb=" N ILE A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN A 490 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 512 through 521 removed outlier: 3.900A pdb=" N ASP A 516 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 519 " --> pdb=" O ARG A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 removed outlier: 3.778A pdb=" N ILE A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 548 removed outlier: 4.649A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER A 547 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.551A pdb=" N ILE A 570 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 571 " --> pdb=" O PRO A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 631 through 645 removed outlier: 4.105A pdb=" N LEU A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 642 " --> pdb=" O GLN A 638 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE A 643 " --> pdb=" O ILE A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.822A pdb=" N VAL A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 710 removed outlier: 3.626A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.868A pdb=" N ASN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS A 725 " --> pdb=" O ASN A 721 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 749 removed outlier: 3.802A pdb=" N VAL A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 796 removed outlier: 3.749A pdb=" N PHE A 796 " --> pdb=" O SER A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 removed outlier: 4.207A pdb=" N LYS A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR A 819 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 821 " --> pdb=" O VAL A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 844 removed outlier: 4.265A pdb=" N SER A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 894 removed outlier: 3.743A pdb=" N MET A 890 " --> pdb=" O ARG A 886 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 893 " --> pdb=" O PRO A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 Processing helix chain 'A' and resid 929 through 938 removed outlier: 3.868A pdb=" N LEU A 938 " --> pdb=" O ALA A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.540A pdb=" N LEU A 964 " --> pdb=" O SER A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 974 through 979 Processing helix chain 'A' and resid 997 through 1004 removed outlier: 3.914A pdb=" N GLU A1001 " --> pdb=" O ASP A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1072 removed outlier: 3.754A pdb=" N LYS A1063 " --> pdb=" O PRO A1059 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 3.651A pdb=" N MET A1092 " --> pdb=" O GLY A1088 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A1093 " --> pdb=" O LYS A1089 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A1098 " --> pdb=" O LYS A1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1141 Processing helix chain 'A' and resid 1224 through 1233 removed outlier: 3.847A pdb=" N GLU A1228 " --> pdb=" O GLN A1224 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A1229 " --> pdb=" O ASP A1225 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A1232 " --> pdb=" O GLU A1228 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A1233 " --> pdb=" O ILE A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1241 removed outlier: 3.541A pdb=" N SER A1240 " --> pdb=" O GLN A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.576A pdb=" N VAL A1246 " --> pdb=" O LYS A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1277 removed outlier: 3.536A pdb=" N TRP A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 removed outlier: 3.626A pdb=" N LEU A1288 " --> pdb=" O GLY A1284 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A1289 " --> pdb=" O TYR A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1318 removed outlier: 4.174A pdb=" N VAL A1316 " --> pdb=" O THR A1312 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1359 removed outlier: 3.779A pdb=" N ARG A1348 " --> pdb=" O THR A1344 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A1349 " --> pdb=" O LYS A1345 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A1352 " --> pdb=" O ARG A1348 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1373 through 1385 removed outlier: 3.623A pdb=" N GLN A1379 " --> pdb=" O THR A1375 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1382 " --> pdb=" O CYS A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1405 removed outlier: 4.011A pdb=" N LEU A1404 " --> pdb=" O THR A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1485 removed outlier: 3.822A pdb=" N GLN A1481 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A1482 " --> pdb=" O PRO A1478 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A1483 " --> pdb=" O LEU A1479 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG A1484 " --> pdb=" O ILE A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1498 through 1505 removed outlier: 3.542A pdb=" N LEU A1502 " --> pdb=" O ASP A1498 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1505 " --> pdb=" O VAL A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1550 removed outlier: 4.237A pdb=" N LEU A1550 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1578 removed outlier: 4.156A pdb=" N ILE A1575 " --> pdb=" O ASP A1571 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A1576 " --> pdb=" O VAL A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1600 Proline residue: A1590 - end of helix removed outlier: 3.661A pdb=" N GLU A1596 " --> pdb=" O VAL A1592 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A1599 " --> pdb=" O SER A1595 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1600 " --> pdb=" O GLU A1596 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1622 removed outlier: 3.586A pdb=" N VAL A1611 " --> pdb=" O ALA A1607 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A1617 " --> pdb=" O SER A1613 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A1622 " --> pdb=" O LEU A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1635 Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.744A pdb=" N GLN A1640 " --> pdb=" O THR A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1642 through 1646 removed outlier: 4.299A pdb=" N VAL A1645 " --> pdb=" O ALA A1642 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A1646 " --> pdb=" O SER A1643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1642 through 1646' Processing helix chain 'A' and resid 1652 through 1668 removed outlier: 3.556A pdb=" N LEU A1665 " --> pdb=" O ASN A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1724 through 1735 removed outlier: 3.549A pdb=" N SER A1728 " --> pdb=" O PRO A1724 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1730 " --> pdb=" O THR A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1736 through 1738 No H-bonds generated for 'chain 'A' and resid 1736 through 1738' Processing helix chain 'A' and resid 1752 through 1764 removed outlier: 3.550A pdb=" N ALA A1759 " --> pdb=" O SER A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1831 Processing helix chain 'A' and resid 1872 through 1877 removed outlier: 3.883A pdb=" N VAL A1876 " --> pdb=" O PRO A1872 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1896 removed outlier: 3.701A pdb=" N LEU A1892 " --> pdb=" O THR A1888 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A1893 " --> pdb=" O SER A1889 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1894 " --> pdb=" O ASP A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 1906 through 1925 removed outlier: 3.537A pdb=" N MET A1911 " --> pdb=" O ILE A1907 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A1912 " --> pdb=" O ILE A1908 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1917 " --> pdb=" O LYS A1913 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A1921 " --> pdb=" O THR A1917 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A1922 " --> pdb=" O LEU A1918 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG A1925 " --> pdb=" O GLN A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1950 removed outlier: 3.820A pdb=" N THR A1942 " --> pdb=" O ASN A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1961 through 1966 removed outlier: 4.185A pdb=" N ASP A1965 " --> pdb=" O ASP A1962 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A1966 " --> pdb=" O PHE A1963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1978 Processing helix chain 'A' and resid 1979 through 1989 removed outlier: 3.726A pdb=" N LEU A1983 " --> pdb=" O ASN A1979 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A1988 " --> pdb=" O LEU A1984 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A1989 " --> pdb=" O ILE A1985 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2046 removed outlier: 3.704A pdb=" N SER A2039 " --> pdb=" O ALA A2035 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A2041 " --> pdb=" O TYR A2037 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A2044 " --> pdb=" O VAL A2040 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A2045 " --> pdb=" O LEU A2041 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A2046 " --> pdb=" O LYS A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2071 removed outlier: 3.578A pdb=" N LEU A2067 " --> pdb=" O THR A2063 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A2070 " --> pdb=" O PHE A2066 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A2071 " --> pdb=" O LEU A2067 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2089 removed outlier: 3.659A pdb=" N ILE A2089 " --> pdb=" O ASP A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2120 removed outlier: 3.894A pdb=" N TYR A2104 " --> pdb=" O ARG A2100 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A2105 " --> pdb=" O GLN A2101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A2115 " --> pdb=" O ASN A2111 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A2119 " --> pdb=" O GLU A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2126 through 2143 removed outlier: 4.336A pdb=" N GLU A2132 " --> pdb=" O THR A2128 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A2136 " --> pdb=" O GLU A2132 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A2137 " --> pdb=" O GLY A2133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN A2142 " --> pdb=" O LYS A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2160 removed outlier: 3.534A pdb=" N ARG A2154 " --> pdb=" O PHE A2150 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2184 removed outlier: 3.969A pdb=" N LEU A2170 " --> pdb=" O GLY A2166 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET A2173 " --> pdb=" O LEU A2169 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A2174 " --> pdb=" O LEU A2170 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A2180 " --> pdb=" O ASN A2176 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A2183 " --> pdb=" O LYS A2179 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A2184 " --> pdb=" O MET A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2185 through 2187 No H-bonds generated for 'chain 'A' and resid 2185 through 2187' Processing helix chain 'A' and resid 2197 through 2206 removed outlier: 3.574A pdb=" N LYS A2201 " --> pdb=" O GLY A2197 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU A2204 " --> pdb=" O VAL A2200 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2227 removed outlier: 3.569A pdb=" N LEU A2225 " --> pdb=" O LEU A2222 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A2226 " --> pdb=" O ASP A2223 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A2227 " --> pdb=" O ARG A2224 " (cutoff:3.500A) Processing helix chain 'A' and resid 2270 through 2274 Processing helix chain 'A' and resid 2284 through 2289 Processing helix chain 'A' and resid 2337 through 2352 removed outlier: 3.975A pdb=" N PHE A2342 " --> pdb=" O ARG A2338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A2344 " --> pdb=" O CYS A2340 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A2345 " --> pdb=" O ILE A2341 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS A2346 " --> pdb=" O PHE A2342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A2348 " --> pdb=" O GLN A2344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A2349 " --> pdb=" O VAL A2345 " (cutoff:3.500A) Processing helix chain 'A' and resid 2370 through 2383 removed outlier: 4.034A pdb=" N GLY A2374 " --> pdb=" O LEU A2370 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A2375 " --> pdb=" O GLY A2371 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A2378 " --> pdb=" O GLY A2374 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS A2383 " --> pdb=" O ASN A2379 " (cutoff:3.500A) Processing helix chain 'A' and resid 2389 through 2403 removed outlier: 3.734A pdb=" N TYR A2396 " --> pdb=" O ALA A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2407 through 2415 removed outlier: 3.584A pdb=" N TYR A2415 " --> pdb=" O ILE A2411 " (cutoff:3.500A) Processing helix chain 'A' and resid 2415 through 2426 removed outlier: 3.770A pdb=" N LEU A2420 " --> pdb=" O LYS A2416 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A2421 " --> pdb=" O PRO A2417 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A2424 " --> pdb=" O LEU A2420 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A2426 " --> pdb=" O PHE A2422 " (cutoff:3.500A) Processing helix chain 'A' and resid 2445 through 2451 removed outlier: 3.705A pdb=" N THR A2449 " --> pdb=" O TYR A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2488 removed outlier: 4.000A pdb=" N TYR A2464 " --> pdb=" O PRO A2460 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A2465 " --> pdb=" O GLU A2461 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU A2466 " --> pdb=" O SER A2462 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU A2469 " --> pdb=" O LEU A2465 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG A2470 " --> pdb=" O LEU A2466 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A2471 " --> pdb=" O SER A2467 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A2473 " --> pdb=" O LEU A2469 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA A2478 " --> pdb=" O ASN A2474 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A2481 " --> pdb=" O ASN A2477 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A2482 " --> pdb=" O ALA A2478 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A2487 " --> pdb=" O ASN A2483 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS A2488 " --> pdb=" O GLU A2484 " (cutoff:3.500A) Processing helix chain 'A' and resid 2495 through 2504 removed outlier: 3.712A pdb=" N SER A2500 " --> pdb=" O TYR A2496 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A2503 " --> pdb=" O LEU A2499 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A2504 " --> pdb=" O SER A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2518 through 2532 removed outlier: 3.665A pdb=" N TYR A2522 " --> pdb=" O PHE A2518 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A2526 " --> pdb=" O TYR A2522 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A2528 " --> pdb=" O ILE A2524 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2551 removed outlier: 3.573A pdb=" N LEU A2551 " --> pdb=" O TYR A2547 " (cutoff:3.500A) Processing helix chain 'A' and resid 2551 through 2561 removed outlier: 3.556A pdb=" N ILE A2555 " --> pdb=" O LEU A2551 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A2558 " --> pdb=" O VAL A2554 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A2559 " --> pdb=" O ILE A2555 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A2561 " --> pdb=" O ALA A2557 " (cutoff:3.500A) Processing helix chain 'A' and resid 2567 through 2579 removed outlier: 3.632A pdb=" N VAL A2571 " --> pdb=" O ALA A2567 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A2572 " --> pdb=" O ARG A2568 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A2577 " --> pdb=" O LYS A2573 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2587 removed outlier: 3.935A pdb=" N SER A2587 " --> pdb=" O LYS A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2919 through 2950 removed outlier: 3.714A pdb=" N TYR A2925 " --> pdb=" O ASP A2921 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A2933 " --> pdb=" O LEU A2929 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A2944 " --> pdb=" O LYS A2940 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A2948 " --> pdb=" O ASN A2944 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER A2950 " --> pdb=" O ARG A2946 " (cutoff:3.500A) Processing helix chain 'A' and resid 2957 through 2961 removed outlier: 3.948A pdb=" N ILE A2961 " --> pdb=" O GLU A2958 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 339 removed outlier: 6.990A pdb=" N MET A 312 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA3, first strand: chain 'A' and resid 673 through 677 removed outlier: 6.544A pdb=" N LEU A 674 " --> pdb=" O LEU A 827 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP A 829 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 676 " --> pdb=" O ASP A 829 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS A 876 " --> pdb=" O LEU A 828 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LEU A 650 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 877 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 652 " --> pdb=" O MET A 877 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A 649 " --> pdb=" O THR A 897 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA5, first strand: chain 'A' and resid 1106 through 1108 removed outlier: 4.037A pdb=" N VAL A1148 " --> pdb=" O ARG A1106 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A1147 " --> pdb=" O PHE A1191 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR A1193 " --> pdb=" O ILE A1147 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU A1149 " --> pdb=" O THR A1193 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A1194 " --> pdb=" O ILE A1081 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1217 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1173 through 1175 removed outlier: 3.895A pdb=" N LEU A1173 " --> pdb=" O VAL A1182 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A1182 " --> pdb=" O LEU A1173 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1488 through 1492 removed outlier: 3.668A pdb=" N PHE A1489 " --> pdb=" O GLN A1534 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A1536 " --> pdb=" O PHE A1489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1769 through 1770 removed outlier: 6.317A pdb=" N ARG A1770 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A1812 " --> pdb=" O PHE A1856 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ALA A1858 " --> pdb=" O VAL A1812 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A1814 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 2006 through 2008 removed outlier: 3.536A pdb=" N VAL A2006 " --> pdb=" O ALA A2013 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A2008 " --> pdb=" O GLU A2011 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A2011 " --> pdb=" O ILE A2008 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 2075 through 2079 removed outlier: 3.607A pdb=" N ILE A2210 " --> pdb=" O ASP A2076 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LEU A2209 " --> pdb=" O PHE A2259 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR A2261 " --> pdb=" O LEU A2209 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A2211 " --> pdb=" O THR A2261 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A2050 " --> pdb=" O LEU A2260 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N MET A2262 " --> pdb=" O LEU A2050 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A2052 " --> pdb=" O MET A2262 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2090 through 2094 removed outlier: 4.447A pdb=" N GLY A2092 " --> pdb=" O PHE A2195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A2195 " --> pdb=" O GLY A2092 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU A2193 " --> pdb=" O GLU A2094 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1371 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: 6.54 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4619 1.34 - 1.46: 1533 1.46 - 1.57: 6283 1.57 - 1.69: 6 1.69 - 1.81: 17 Bond restraints: 12458 Sorted by residual: bond pdb=" C UNK A 30 " pdb=" N UNK A 31 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.40e-02 5.10e+03 4.33e+00 bond pdb=" C UNK A 23 " pdb=" N UNK A 24 " ideal model delta sigma weight residual 1.329 1.350 -0.021 1.40e-02 5.10e+03 2.29e+00 bond pdb=" C GLU A 863 " pdb=" O GLU A 863 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.22e+00 bond pdb=" C LEU A2447 " pdb=" N PRO A2448 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.25e-02 6.40e+03 1.50e+00 bond pdb=" N PRO A2219 " pdb=" CA PRO A2219 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.43e+00 ... (remaining 12453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 16667 1.74 - 3.48: 483 3.48 - 5.22: 82 5.22 - 6.96: 23 6.96 - 8.70: 10 Bond angle restraints: 17265 Sorted by residual: angle pdb=" C UNK A 30 " pdb=" N UNK A 31 " pdb=" CA UNK A 31 " ideal model delta sigma weight residual 121.70 113.00 8.70 1.80e+00 3.09e-01 2.34e+01 angle pdb=" N VAL A2407 " pdb=" CA VAL A2407 " pdb=" C VAL A2407 " ideal model delta sigma weight residual 113.53 109.18 4.35 9.80e-01 1.04e+00 1.97e+01 angle pdb=" C ASP A2212 " pdb=" N ASN A2213 " pdb=" CA ASN A2213 " ideal model delta sigma weight residual 121.54 129.21 -7.67 1.91e+00 2.74e-01 1.61e+01 angle pdb=" CA TYR A2005 " pdb=" CB TYR A2005 " pdb=" CG TYR A2005 " ideal model delta sigma weight residual 113.90 120.76 -6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" C LYS A 734 " pdb=" N ASN A 735 " pdb=" CA ASN A 735 " ideal model delta sigma weight residual 121.19 127.10 -5.91 1.59e+00 3.96e-01 1.38e+01 ... (remaining 17260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.96: 7254 28.96 - 57.92: 31 57.92 - 86.87: 3 86.87 - 115.83: 0 115.83 - 144.79: 4 Dihedral angle restraints: 7292 sinusoidal: 674 harmonic: 6618 Sorted by residual: dihedral pdb=" CA THR A2024 " pdb=" C THR A2024 " pdb=" N GLN A2025 " pdb=" CA GLN A2025 " ideal model delta harmonic sigma weight residual -180.00 -142.99 -37.01 0 5.00e+00 4.00e-02 5.48e+01 dihedral pdb=" C5' ADP A5002 " pdb=" O5' ADP A5002 " pdb=" PA ADP A5002 " pdb=" O2A ADP A5002 " ideal model delta sinusoidal sigma weight residual 300.00 155.22 144.79 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O2A ADP A5001 " pdb=" O3A ADP A5001 " pdb=" PA ADP A5001 " pdb=" PB ADP A5001 " ideal model delta sinusoidal sigma weight residual -60.00 83.49 -143.49 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 7289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1985 0.065 - 0.130: 309 0.130 - 0.195: 7 0.195 - 0.260: 1 0.260 - 0.325: 1 Chirality restraints: 2303 Sorted by residual: chirality pdb=" CB ILE A2961 " pdb=" CA ILE A2961 " pdb=" CG1 ILE A2961 " pdb=" CG2 ILE A2961 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ARG A2271 " pdb=" N ARG A2271 " pdb=" C ARG A2271 " pdb=" CB ARG A2271 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA TYR A2005 " pdb=" N TYR A2005 " pdb=" C TYR A2005 " pdb=" CB TYR A2005 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 2300 not shown) Planarity restraints: 2381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 460 " 0.048 5.00e-02 4.00e+02 7.26e-02 8.44e+00 pdb=" N PRO A 461 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 461 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 461 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2459 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.32e+00 pdb=" N PRO A2460 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A2460 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2460 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A2054 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A2055 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A2055 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A2055 " 0.028 5.00e-02 4.00e+02 ... (remaining 2378 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 20 2.53 - 3.13: 7763 3.13 - 3.72: 17979 3.72 - 4.31: 19479 4.31 - 4.90: 31954 Nonbonded interactions: 77195 Sorted by model distance: nonbonded pdb=" O GLU A 804 " pdb=" N SER A 806 " model vdw 1.943 3.120 nonbonded pdb=" OG1 THR A2061 " pdb=" O3B ADP A5002 " model vdw 2.128 3.040 nonbonded pdb=" OG1 THR A 322 " pdb=" O1B ADP A5001 " model vdw 2.204 3.040 nonbonded pdb=" O LYS A 316 " pdb=" NZ LYS A 321 " model vdw 2.238 3.120 nonbonded pdb=" OG1 THR A2002 " pdb=" O ASP A2004 " model vdw 2.345 3.040 ... (remaining 77190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.860 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.130 Process input model: 37.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 : 0.003 0.034 12458 Z= 0.158 Angle : 0.719 8.700 17265 Z= 0.395 Chirality : 0.046 0.325 2303 Planarity : 0.004 0.073 2381 Dihedral : 8.718 144.787 2944 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.31 % Favored : 92.25 % Rotamer: Outliers : 0.34 % Allowed : 6.44 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.99 (0.12), residues: 2038 helix: -5.01 (0.04), residues: 776 sheet: -2.06 (0.35), residues: 181 loop : -3.56 (0.15), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 381 HIS 0.003 0.001 HIS A2018 PHE 0.023 0.001 PHE A 288 TYR 0.024 0.001 TYR A2005 ARG 0.003 0.000 ARG A2470 Details of bonding type rmsd hydrogen bonds : bond 0.34189 ( 476) hydrogen bonds : angle 9.78005 ( 1371) covalent geometry : bond 0.00265 (12458) covalent geometry : angle 0.71947 (17265) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 2012 VAL cc_start: 0.9083 (t) cc_final: 0.8811 (m) REVERT: A 2209 LEU cc_start: 0.9221 (mm) cc_final: 0.8399 (tt) REVERT: A 2405 MET cc_start: 0.8054 (mpt) cc_final: 0.6886 (tpt) REVERT: A 2473 LEU cc_start: 0.9126 (tt) cc_final: 0.8742 (tp) REVERT: A 2939 MET cc_start: 0.8589 (tpp) cc_final: 0.8186 (tpp) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.2381 time to fit residues: 44.5386 Evaluate side-chains 82 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 5.9990 chunk 172 optimal weight: 0.0770 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 overall best weight: 3.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2944 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086601 restraints weight = 51914.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085863 restraints weight = 89859.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.086124 restraints weight = 82449.066| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 12458 Z= 0.390 Angle : 0.936 10.506 17265 Z= 0.492 Chirality : 0.050 0.228 2303 Planarity : 0.006 0.069 2381 Dihedral : 8.556 145.112 2305 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.92 % Favored : 87.83 % Rotamer: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.23 (0.16), residues: 2038 helix: -2.47 (0.14), residues: 826 sheet: -2.46 (0.36), residues: 175 loop : -3.20 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP A 381 HIS 0.014 0.004 HIS A2018 PHE 0.029 0.003 PHE A2066 TYR 0.025 0.003 TYR A2005 ARG 0.007 0.002 ARG A1944 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 476) hydrogen bonds : angle 5.91297 ( 1371) covalent geometry : bond 0.00778 (12458) covalent geometry : angle 0.93605 (17265) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.318 Fit side-chains REVERT: A 818 LYS cc_start: 0.9162 (tppt) cc_final: 0.8595 (tptp) REVERT: A 877 MET cc_start: 0.7804 (tpt) cc_final: 0.7509 (mmm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1492 time to fit residues: 19.2068 Evaluate side-chains 62 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 116 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 200 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 202 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 164 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.107665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090000 restraints weight = 51224.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088780 restraints weight = 72604.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.089242 restraints weight = 64026.164| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12458 Z= 0.102 Angle : 0.537 7.633 17265 Z= 0.279 Chirality : 0.041 0.162 2303 Planarity : 0.003 0.053 2381 Dihedral : 7.216 147.493 2305 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.24 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.99 (0.18), residues: 2038 helix: -1.00 (0.18), residues: 813 sheet: -1.95 (0.39), residues: 168 loop : -2.87 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 381 HIS 0.004 0.002 HIS A 292 PHE 0.011 0.001 PHE A2398 TYR 0.021 0.001 TYR A2005 ARG 0.002 0.000 ARG A2470 Details of bonding type rmsd hydrogen bonds : bond 0.02817 ( 476) hydrogen bonds : angle 4.11034 ( 1371) covalent geometry : bond 0.00200 (12458) covalent geometry : angle 0.53713 (17265) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.157 Fit side-chains REVERT: A 818 LYS cc_start: 0.9073 (tppt) cc_final: 0.8567 (tptp) REVERT: A 874 PHE cc_start: 0.7975 (m-80) cc_final: 0.7744 (m-80) REVERT: A 877 MET cc_start: 0.7624 (tpt) cc_final: 0.7009 (tmm) REVERT: A 2012 VAL cc_start: 0.9145 (t) cc_final: 0.8871 (m) REVERT: A 2053 VAL cc_start: 0.9094 (t) cc_final: 0.8880 (m) REVERT: A 2473 LEU cc_start: 0.9024 (tt) cc_final: 0.8741 (tp) REVERT: A 2954 GLU cc_start: 0.8541 (tp30) cc_final: 0.8170 (tp30) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2057 time to fit residues: 28.9175 Evaluate side-chains 72 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 166 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 115 optimal weight: 0.9980 chunk 211 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 216 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 76 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.108936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.091747 restraints weight = 50706.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090282 restraints weight = 69213.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090743 restraints weight = 61595.170| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12458 Z= 0.079 Angle : 0.499 9.341 17265 Z= 0.253 Chirality : 0.041 0.157 2303 Planarity : 0.003 0.041 2381 Dihedral : 6.584 147.330 2305 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.03 % Favored : 90.82 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.03 (0.19), residues: 2038 helix: 0.09 (0.19), residues: 793 sheet: -1.52 (0.42), residues: 165 loop : -2.54 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 381 HIS 0.003 0.001 HIS A2369 PHE 0.015 0.001 PHE A 288 TYR 0.021 0.001 TYR A2005 ARG 0.002 0.000 ARG A2470 Details of bonding type rmsd hydrogen bonds : bond 0.02060 ( 476) hydrogen bonds : angle 3.44801 ( 1371) covalent geometry : bond 0.00156 (12458) covalent geometry : angle 0.49873 (17265) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.320 Fit side-chains REVERT: A 818 LYS cc_start: 0.9072 (tppt) cc_final: 0.8513 (tptp) REVERT: A 877 MET cc_start: 0.7731 (tpt) cc_final: 0.7077 (tmm) REVERT: A 2012 VAL cc_start: 0.9207 (t) cc_final: 0.8888 (m) REVERT: A 2053 VAL cc_start: 0.9076 (t) cc_final: 0.8857 (m) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1654 time to fit residues: 24.3255 Evaluate side-chains 76 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 0.8980 chunk 130 optimal weight: 0.0000 chunk 5 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 210 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 199 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.106734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089241 restraints weight = 50939.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088309 restraints weight = 66888.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.088773 restraints weight = 62626.749| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12458 Z= 0.129 Angle : 0.551 7.919 17265 Z= 0.281 Chirality : 0.042 0.166 2303 Planarity : 0.003 0.043 2381 Dihedral : 6.716 139.128 2305 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.06 % Favored : 89.79 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.79 (0.19), residues: 2038 helix: 0.36 (0.20), residues: 805 sheet: -1.45 (0.44), residues: 152 loop : -2.48 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 381 HIS 0.004 0.001 HIS A2286 PHE 0.011 0.001 PHE A2066 TYR 0.019 0.001 TYR A2005 ARG 0.002 0.000 ARG A2114 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 476) hydrogen bonds : angle 3.77979 ( 1371) covalent geometry : bond 0.00260 (12458) covalent geometry : angle 0.55116 (17265) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.387 Fit side-chains REVERT: A 818 LYS cc_start: 0.9086 (tppt) cc_final: 0.8531 (tptp) REVERT: A 877 MET cc_start: 0.7859 (tpt) cc_final: 0.7620 (mmm) REVERT: A 2012 VAL cc_start: 0.9169 (t) cc_final: 0.8847 (m) REVERT: A 2936 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 2954 GLU cc_start: 0.8438 (tp30) cc_final: 0.8223 (tp30) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1741 time to fit residues: 24.0316 Evaluate side-chains 71 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 69 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 154 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.103032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086374 restraints weight = 52166.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085336 restraints weight = 78754.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085731 restraints weight = 75227.026| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12458 Z= 0.250 Angle : 0.736 8.962 17265 Z= 0.379 Chirality : 0.046 0.205 2303 Planarity : 0.004 0.051 2381 Dihedral : 7.861 140.227 2305 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.64 % Favored : 86.16 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.19), residues: 2038 helix: -0.21 (0.18), residues: 830 sheet: -1.82 (0.43), residues: 150 loop : -2.71 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 381 HIS 0.008 0.003 HIS A 292 PHE 0.020 0.002 PHE A1998 TYR 0.020 0.002 TYR A2005 ARG 0.005 0.001 ARG A2114 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 476) hydrogen bonds : angle 5.05216 ( 1371) covalent geometry : bond 0.00509 (12458) covalent geometry : angle 0.73607 (17265) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.307 Fit side-chains REVERT: A 818 LYS cc_start: 0.8989 (tppt) cc_final: 0.8396 (tptp) REVERT: A 877 MET cc_start: 0.7845 (tpt) cc_final: 0.7574 (mmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1562 time to fit residues: 20.4520 Evaluate side-chains 68 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 208 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 112 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.104089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087476 restraints weight = 52068.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086567 restraints weight = 80431.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086891 restraints weight = 76545.210| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12458 Z= 0.180 Angle : 0.626 10.108 17265 Z= 0.321 Chirality : 0.044 0.216 2303 Planarity : 0.003 0.052 2381 Dihedral : 7.412 139.720 2305 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.33 % Favored : 88.52 % Rotamer: Outliers : 0.34 % Allowed : 2.37 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.01 (0.19), residues: 2038 helix: 0.15 (0.19), residues: 821 sheet: -1.73 (0.47), residues: 130 loop : -2.58 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 381 HIS 0.004 0.002 HIS A2286 PHE 0.017 0.001 PHE A2398 TYR 0.019 0.002 TYR A2005 ARG 0.003 0.001 ARG A1944 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 476) hydrogen bonds : angle 4.42683 ( 1371) covalent geometry : bond 0.00365 (12458) covalent geometry : angle 0.62615 (17265) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.328 Fit side-chains REVERT: A 818 LYS cc_start: 0.8936 (tppt) cc_final: 0.8325 (tptp) REVERT: A 877 MET cc_start: 0.7849 (tpt) cc_final: 0.7603 (mmm) REVERT: A 2473 LEU cc_start: 0.9153 (tp) cc_final: 0.8926 (tp) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1739 time to fit residues: 23.3535 Evaluate side-chains 69 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 138 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 39 optimal weight: 0.0030 chunk 87 optimal weight: 0.5980 chunk 214 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.105197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088186 restraints weight = 51689.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.087223 restraints weight = 67020.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087693 restraints weight = 64805.827| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12458 Z= 0.121 Angle : 0.565 10.948 17265 Z= 0.286 Chirality : 0.042 0.181 2303 Planarity : 0.003 0.049 2381 Dihedral : 6.992 138.738 2305 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.63 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.66 (0.20), residues: 2038 helix: 0.56 (0.20), residues: 822 sheet: -1.66 (0.45), residues: 141 loop : -2.49 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 381 HIS 0.003 0.001 HIS A2369 PHE 0.013 0.001 PHE A2398 TYR 0.017 0.001 TYR A2005 ARG 0.003 0.001 ARG A2946 Details of bonding type rmsd hydrogen bonds : bond 0.02546 ( 476) hydrogen bonds : angle 3.97495 ( 1371) covalent geometry : bond 0.00245 (12458) covalent geometry : angle 0.56491 (17265) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.234 Fit side-chains REVERT: A 818 LYS cc_start: 0.8919 (tppt) cc_final: 0.8225 (tptp) REVERT: A 877 MET cc_start: 0.7837 (tpt) cc_final: 0.7604 (mmm) REVERT: A 2224 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8351 (tpt170) REVERT: A 2954 GLU cc_start: 0.8584 (tp30) cc_final: 0.8087 (tp30) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1642 time to fit residues: 22.8029 Evaluate side-chains 73 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 107 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 0.1980 chunk 209 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 186 optimal weight: 0.0370 chunk 138 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 overall best weight: 1.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087259 restraints weight = 51627.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.086726 restraints weight = 71216.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087076 restraints weight = 63113.794| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12458 Z= 0.192 Angle : 0.647 11.785 17265 Z= 0.330 Chirality : 0.044 0.192 2303 Planarity : 0.003 0.050 2381 Dihedral : 7.405 134.740 2305 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.69 % Favored : 86.21 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.80 (0.20), residues: 2038 helix: 0.41 (0.19), residues: 818 sheet: -1.78 (0.46), residues: 132 loop : -2.51 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 381 HIS 0.004 0.002 HIS A2286 PHE 0.019 0.001 PHE A1998 TYR 0.050 0.002 TYR A2005 ARG 0.003 0.001 ARG A2114 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 476) hydrogen bonds : angle 4.48831 ( 1371) covalent geometry : bond 0.00393 (12458) covalent geometry : angle 0.64737 (17265) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.249 Fit side-chains REVERT: A 818 LYS cc_start: 0.8948 (tppt) cc_final: 0.8269 (tptp) REVERT: A 877 MET cc_start: 0.7953 (tpt) cc_final: 0.7715 (mmm) REVERT: A 2224 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8447 (tpt170) REVERT: A 2473 LEU cc_start: 0.9193 (tp) cc_final: 0.8977 (tp) REVERT: A 2954 GLU cc_start: 0.8620 (tp30) cc_final: 0.8229 (tp30) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1613 time to fit residues: 21.4269 Evaluate side-chains 69 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 143 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 215 optimal weight: 0.0170 chunk 197 optimal weight: 0.9980 chunk 153 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 overall best weight: 2.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.102318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085484 restraints weight = 51788.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084736 restraints weight = 70595.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085002 restraints weight = 76603.822| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12458 Z= 0.240 Angle : 0.713 12.414 17265 Z= 0.367 Chirality : 0.045 0.205 2303 Planarity : 0.004 0.057 2381 Dihedral : 7.866 143.121 2305 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.77 % Favored : 85.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.07 (0.19), residues: 2038 helix: 0.13 (0.19), residues: 818 sheet: -2.04 (0.45), residues: 131 loop : -2.60 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 381 HIS 0.005 0.002 HIS A2286 PHE 0.019 0.002 PHE A1998 TYR 0.045 0.002 TYR A2005 ARG 0.005 0.001 ARG A2394 Details of bonding type rmsd hydrogen bonds : bond 0.03701 ( 476) hydrogen bonds : angle 4.96563 ( 1371) covalent geometry : bond 0.00487 (12458) covalent geometry : angle 0.71301 (17265) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4076 Ramachandran restraints generated. 2038 Oldfield, 0 Emsley, 2038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.394 Fit side-chains REVERT: A 818 LYS cc_start: 0.9035 (tppt) cc_final: 0.8323 (tptp) REVERT: A 877 MET cc_start: 0.7885 (tpt) cc_final: 0.7636 (mmm) REVERT: A 2224 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8498 (tpt170) REVERT: A 2473 LEU cc_start: 0.9247 (tp) cc_final: 0.9033 (tp) REVERT: A 2954 GLU cc_start: 0.8662 (tp30) cc_final: 0.8298 (tp30) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1737 time to fit residues: 22.9959 Evaluate side-chains 69 residues out of total 1871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 136 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.085551 restraints weight = 52231.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.085373 restraints weight = 74143.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085314 restraints weight = 74855.415| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12458 Z= 0.248 Angle : 0.722 10.831 17265 Z= 0.373 Chirality : 0.046 0.195 2303 Planarity : 0.004 0.059 2381 Dihedral : 7.988 145.874 2305 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 14.57 % Favored : 85.28 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.22 (0.19), residues: 2038 helix: 0.03 (0.19), residues: 800 sheet: -2.26 (0.43), residues: 139 loop : -2.64 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 381 HIS 0.005 0.002 HIS A2253 PHE 0.022 0.002 PHE A1998 TYR 0.042 0.002 TYR A2005 ARG 0.004 0.001 ARG A1944 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 476) hydrogen bonds : angle 5.06057 ( 1371) covalent geometry : bond 0.00506 (12458) covalent geometry : angle 0.72227 (17265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3312.58 seconds wall clock time: 58 minutes 40.54 seconds (3520.54 seconds total)