Starting phenix.real_space_refine on Mon Apr 15 02:02:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yz0_6862/04_2024/5yz0_6862.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yz0_6862/04_2024/5yz0_6862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yz0_6862/04_2024/5yz0_6862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yz0_6862/04_2024/5yz0_6862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yz0_6862/04_2024/5yz0_6862.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yz0_6862/04_2024/5yz0_6862.pdb" } resolution = 4.7 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 20633 2.51 5 N 6250 2.21 5 O 6364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2333": "NH1" <-> "NH2" Residue "A TYR 2400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2333": "NH1" <-> "NH2" Residue "B TYR 2400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2643": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33371 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 15007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2362, 15007 Classifications: {'peptide': 2362} Incomplete info: {'truncation_to_alanine': 1186} Link IDs: {'CIS': 12, 'PTRANS': 87, 'TRANS': 2262} Chain breaks: 8 Unresolved chain link angles: 48 Unresolved non-hydrogen bonds: 4131 Unresolved non-hydrogen angles: 5248 Unresolved non-hydrogen dihedrals: 3450 Unresolved non-hydrogen chiralities: 404 Planarities with less than four sites: {'GLN:plan1': 56, 'ASP:plan': 64, 'TYR:plan': 36, 'ASN:plan1': 43, 'TRP:plan': 12, 'HIS:plan': 38, 'PHE:plan': 60, 'GLU:plan': 83, 'ARG:plan': 55} Unresolved non-hydrogen planarities: 2062 Chain: "B" Number of atoms: 15007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2362, 15007 Classifications: {'peptide': 2362} Incomplete info: {'truncation_to_alanine': 1186} Link IDs: {'CIS': 12, 'PTRANS': 87, 'TRANS': 2262} Chain breaks: 8 Unresolved chain link angles: 48 Unresolved non-hydrogen bonds: 4131 Unresolved non-hydrogen angles: 5248 Unresolved non-hydrogen dihedrals: 3450 Unresolved non-hydrogen chiralities: 404 Planarities with less than four sites: {'GLN:plan1': 56, 'ASP:plan': 64, 'TYR:plan': 36, 'ASN:plan1': 43, 'TRP:plan': 12, 'HIS:plan': 38, 'PHE:plan': 60, 'GLU:plan': 83, 'ARG:plan': 55} Unresolved non-hydrogen planarities: 2062 Chain: "C" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 1785 Classifications: {'peptide': 362} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 311} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 328} Unresolved chain link angles: 32 Unresolved non-hydrogen bonds: 1048 Unresolved non-hydrogen angles: 1309 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 20, 'HIS:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 12, 'GLU:plan': 30, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 522 Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 1572 Classifications: {'peptide': 318} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 277} Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 288} Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 960 Unresolved non-hydrogen angles: 1198 Unresolved non-hydrogen dihedrals: 802 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 19, 'HIS:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 29, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 498 Time building chain proxies: 18.80, per 1000 atoms: 0.56 Number of scatterers: 33371 At special positions: 0 Unit cell: (145.6, 208, 195, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 6364 8.00 N 6250 7.00 C 20633 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A2226 " - pdb=" SG CYS A2326 " distance=2.04 Simple disulfide: pdb=" SG CYS B2226 " - pdb=" SG CYS B2326 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.10 Conformation dependent library (CDL) restraints added in 7.8 seconds 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10326 Finding SS restraints... Secondary structure from input PDB file: 297 helices and 4 sheets defined 70.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 26 through 44 Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 50 through 71 removed outlier: 3.693A pdb=" N LYS A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 77 through 91 removed outlier: 4.203A pdb=" N HIS A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 96 through 120 removed outlier: 3.645A pdb=" N ILE A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.789A pdb=" N LEU A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 142 Proline residue: A 139 - end of helix Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 155 through 166 removed outlier: 4.021A pdb=" N HIS A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 188 removed outlier: 3.884A pdb=" N MET A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 removed outlier: 4.088A pdb=" N MET A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 207 " --> pdb=" O GLU A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 230 removed outlier: 3.508A pdb=" N LEU A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 262 through 280 Processing helix chain 'A' and resid 284 through 303 removed outlier: 3.580A pdb=" N LYS A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) Proline residue: A 294 - end of helix Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 337 through 356 removed outlier: 3.602A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 382 removed outlier: 3.608A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 396 Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 397 through 414 removed outlier: 3.526A pdb=" N MET A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 Proline residue: A 429 - end of helix removed outlier: 3.614A pdb=" N LEU A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 439 " --> pdb=" O SER A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 447 through 459 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 483 through 500 removed outlier: 3.583A pdb=" N VAL A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 516 removed outlier: 3.930A pdb=" N CYS A 507 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 537 removed outlier: 3.812A pdb=" N LYS A 527 " --> pdb=" O LYS A 523 " (cutoff:3.500A) Proline residue: A 528 - end of helix removed outlier: 3.806A pdb=" N THR A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 559 Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.729A pdb=" N MET A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 596 removed outlier: 3.548A pdb=" N HIS A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 613 removed outlier: 3.795A pdb=" N CYS A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 Proline residue: A 630 - end of helix Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 641 through 653 removed outlier: 3.897A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP A 651 " --> pdb=" O ILE A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 Processing helix chain 'A' and resid 664 through 678 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.810A pdb=" N VAL A 688 " --> pdb=" O SER A 684 " (cutoff:3.500A) Proline residue: A 689 - end of helix Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 702 through 716 Processing helix chain 'A' and resid 716 through 721 removed outlier: 4.021A pdb=" N GLY A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 716 through 721' Processing helix chain 'A' and resid 723 through 739 removed outlier: 4.191A pdb=" N THR A 729 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) Proline residue: A 731 - end of helix Processing helix chain 'A' and resid 748 through 762 removed outlier: 3.600A pdb=" N GLU A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N CYS A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 761 " --> pdb=" O GLN A 757 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 762 " --> pdb=" O LEU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.583A pdb=" N ALA A 781 " --> pdb=" O PRO A 777 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 782 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 808 Processing helix chain 'A' and resid 813 through 826 removed outlier: 3.686A pdb=" N ARG A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 839 Processing helix chain 'A' and resid 841 through 848 removed outlier: 4.103A pdb=" N LEU A 845 " --> pdb=" O PHE A 841 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 866 removed outlier: 3.969A pdb=" N LYS A 866 " --> pdb=" O ASN A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 removed outlier: 3.822A pdb=" N VAL A 885 " --> pdb=" O LYS A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 904 removed outlier: 4.153A pdb=" N VAL A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 929 Processing helix chain 'A' and resid 934 through 946 removed outlier: 4.265A pdb=" N VAL A 938 " --> pdb=" O CYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 969 removed outlier: 3.767A pdb=" N ARG A 968 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 969 " --> pdb=" O ALA A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 991 removed outlier: 3.593A pdb=" N ALA A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Proline residue: A 985 - end of helix Processing helix chain 'A' and resid 997 through 1012 Proline residue: A1008 - end of helix Processing helix chain 'A' and resid 1014 through 1030 removed outlier: 3.992A pdb=" N GLN A1020 " --> pdb=" O THR A1016 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A1023 " --> pdb=" O LYS A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1049 removed outlier: 4.172A pdb=" N LEU A1040 " --> pdb=" O ILE A1036 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1068 Processing helix chain 'A' and resid 1103 through 1118 Proline residue: A1110 - end of helix Proline residue: A1116 - end of helix Processing helix chain 'A' and resid 1122 through 1137 removed outlier: 3.639A pdb=" N GLY A1129 " --> pdb=" O PRO A1125 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'A' and resid 1152 through 1163 removed outlier: 3.788A pdb=" N MET A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1182 removed outlier: 3.562A pdb=" N THR A1177 " --> pdb=" O LYS A1173 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A1178 " --> pdb=" O MET A1174 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A1179 " --> pdb=" O MET A1175 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A1181 " --> pdb=" O THR A1177 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A1182 " --> pdb=" O LEU A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1398 Processing helix chain 'A' and resid 1400 through 1414 removed outlier: 4.651A pdb=" N ALA A1408 " --> pdb=" O TYR A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1434 Processing helix chain 'A' and resid 1438 through 1444 removed outlier: 3.805A pdb=" N LEU A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1455 Processing helix chain 'A' and resid 1474 through 1482 Processing helix chain 'A' and resid 1486 through 1499 Processing helix chain 'A' and resid 1503 through 1520 removed outlier: 4.101A pdb=" N SER A1515 " --> pdb=" O PHE A1511 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A1516 " --> pdb=" O THR A1512 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET A1518 " --> pdb=" O CYS A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1539 removed outlier: 4.131A pdb=" N THR A1525 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A1526 " --> pdb=" O PHE A1522 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A1527 " --> pdb=" O LYS A1523 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU A1528 " --> pdb=" O VAL A1524 " (cutoff:3.500A) Proline residue: A1530 - end of helix removed outlier: 3.647A pdb=" N LEU A1533 " --> pdb=" O LEU A1529 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A1539 " --> pdb=" O TYR A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1542 through 1559 removed outlier: 3.563A pdb=" N LEU A1556 " --> pdb=" O ILE A1552 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS A1557 " --> pdb=" O MET A1553 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N HIS A1558 " --> pdb=" O ALA A1554 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP A1559 " --> pdb=" O VAL A1555 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1603 removed outlier: 3.766A pdb=" N VAL A1581 " --> pdb=" O SER A1577 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS A1587 " --> pdb=" O SER A1583 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1603 " --> pdb=" O LEU A1599 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1636 removed outlier: 3.732A pdb=" N ILE A1636 " --> pdb=" O PHE A1632 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1648 removed outlier: 4.012A pdb=" N ALA A1644 " --> pdb=" O THR A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1664 removed outlier: 3.806A pdb=" N VAL A1655 " --> pdb=" O TYR A1651 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A1659 " --> pdb=" O VAL A1655 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER A1660 " --> pdb=" O MET A1656 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A1661 " --> pdb=" O HIS A1657 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A1664 " --> pdb=" O SER A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1682 removed outlier: 5.315A pdb=" N GLY A1674 " --> pdb=" O GLN A1670 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE A1675 " --> pdb=" O GLU A1671 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A1676 " --> pdb=" O HIS A1672 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A1677 " --> pdb=" O LEU A1673 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS A1678 " --> pdb=" O GLY A1674 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A1679 " --> pdb=" O PHE A1675 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A1682 " --> pdb=" O LYS A1678 " (cutoff:3.500A) Processing helix chain 'A' and resid 1685 through 1694 removed outlier: 4.304A pdb=" N VAL A1689 " --> pdb=" O GLU A1685 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A1690 " --> pdb=" O PRO A1686 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY A1691 " --> pdb=" O ASP A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1701 through 1713 removed outlier: 3.864A pdb=" N GLN A1705 " --> pdb=" O SER A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1717 through 1727 removed outlier: 4.114A pdb=" N CYS A1721 " --> pdb=" O ASP A1717 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A1724 " --> pdb=" O ALA A1720 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A1725 " --> pdb=" O CYS A1721 " (cutoff:3.500A) Processing helix chain 'A' and resid 1733 through 1746 removed outlier: 3.702A pdb=" N LYS A1741 " --> pdb=" O HIS A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1748 through 1763 removed outlier: 3.917A pdb=" N THR A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A1757 " --> pdb=" O ILE A1753 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A1758 " --> pdb=" O THR A1754 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL A1759 " --> pdb=" O GLN A1755 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N HIS A1760 " --> pdb=" O VAL A1756 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A1761 " --> pdb=" O ASN A1757 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A1762 " --> pdb=" O GLY A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1771 removed outlier: 3.537A pdb=" N LEU A1770 " --> pdb=" O THR A1767 " (cutoff:3.500A) Processing helix chain 'A' and resid 1784 through 1791 Processing helix chain 'A' and resid 1799 through 1813 removed outlier: 4.206A pdb=" N LEU A1807 " --> pdb=" O ARG A1803 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A1808 " --> pdb=" O LEU A1804 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A1809 " --> pdb=" O GLY A1805 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1810 " --> pdb=" O GLN A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1815 through 1835 removed outlier: 4.003A pdb=" N TYR A1820 " --> pdb=" O ILE A1816 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A1823 " --> pdb=" O PHE A1819 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A1828 " --> pdb=" O LYS A1824 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1831 " --> pdb=" O ARG A1827 " (cutoff:3.500A) Proline residue: A1833 - end of helix Processing helix chain 'A' and resid 1842 through 1846 removed outlier: 3.793A pdb=" N GLN A1845 " --> pdb=" O GLY A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1869 removed outlier: 3.936A pdb=" N LEU A1857 " --> pdb=" O ARG A1853 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS A1858 " --> pdb=" O LEU A1854 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU A1859 " --> pdb=" O HIS A1855 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU A1860 " --> pdb=" O MET A1856 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER A1863 " --> pdb=" O GLU A1859 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS A1865 " --> pdb=" O GLU A1861 " (cutoff:3.500A) Proline residue: A1866 - end of helix removed outlier: 3.515A pdb=" N GLN A1869 " --> pdb=" O LYS A1865 " (cutoff:3.500A) Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.607A pdb=" N ARG A1895 " --> pdb=" O ASN A1892 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A1897 " --> pdb=" O TYR A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1904 through 1913 Processing helix chain 'A' and resid 1914 through 1916 No H-bonds generated for 'chain 'A' and resid 1914 through 1916' Processing helix chain 'A' and resid 1922 through 1937 removed outlier: 4.432A pdb=" N GLN A1926 " --> pdb=" O GLU A1922 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A1928 " --> pdb=" O TRP A1924 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N HIS A1937 " --> pdb=" O LYS A1933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1945 through 1951 removed outlier: 3.960A pdb=" N GLU A1949 " --> pdb=" O LEU A1945 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A1950 " --> pdb=" O ASN A1946 " (cutoff:3.500A) Processing helix chain 'A' and resid 1958 through 1973 removed outlier: 3.878A pdb=" N SER A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A1966 " --> pdb=" O TRP A1962 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A1967 " --> pdb=" O LEU A1963 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A1968 " --> pdb=" O TRP A1964 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A1969 " --> pdb=" O SER A1965 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS A1970 " --> pdb=" O LYS A1966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1975 through 1983 removed outlier: 4.352A pdb=" N GLY A1979 " --> pdb=" O VAL A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 1989 Processing helix chain 'A' and resid 1997 through 2002 Processing helix chain 'A' and resid 2005 through 2010 Processing helix chain 'A' and resid 2012 through 2017 removed outlier: 4.016A pdb=" N PHE A2016 " --> pdb=" O GLU A2012 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU A2017 " --> pdb=" O THR A2013 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2012 through 2017' Processing helix chain 'A' and resid 2021 through 2032 removed outlier: 3.538A pdb=" N TYR A2025 " --> pdb=" O ILE A2021 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A2030 " --> pdb=" O LYS A2026 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A2032 " --> pdb=" O VAL A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2032 through 2037 Processing helix chain 'A' and resid 2043 through 2057 removed outlier: 4.093A pdb=" N LYS A2048 " --> pdb=" O LYS A2044 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A2049 " --> pdb=" O TYR A2045 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET A2050 " --> pdb=" O TYR A2046 " (cutoff:3.500A) Proline residue: A2051 - end of helix removed outlier: 3.719A pdb=" N ASP A2055 " --> pdb=" O PRO A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2063 through 2078 removed outlier: 4.432A pdb=" N TYR A2067 " --> pdb=" O ASP A2063 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A2071 " --> pdb=" O TYR A2067 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N PHE A2072 " --> pdb=" O ILE A2068 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A2076 " --> pdb=" O PHE A2072 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN A2077 " --> pdb=" O GLY A2073 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A2078 " --> pdb=" O ARG A2074 " (cutoff:3.500A) Processing helix chain 'A' and resid 2086 through 2109 removed outlier: 3.928A pdb=" N MET A2090 " --> pdb=" O SER A2086 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA A2101 " --> pdb=" O TYR A2097 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A2102 " --> pdb=" O GLY A2098 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A2103 " --> pdb=" O THR A2099 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A2108 " --> pdb=" O TRP A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2111 through 2133 removed outlier: 4.176A pdb=" N ASN A2117 " --> pdb=" O VAL A2113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A2127 " --> pdb=" O ASN A2123 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A2128 " --> pdb=" O LYS A2124 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A2129 " --> pdb=" O VAL A2125 " (cutoff:3.500A) Processing helix chain 'A' and resid 2134 through 2139 removed outlier: 4.243A pdb=" N PHE A2138 " --> pdb=" O ALA A2134 " (cutoff:3.500A) Processing helix chain 'A' and resid 2141 through 2148 removed outlier: 3.906A pdb=" N ARG A2148 " --> pdb=" O GLN A2144 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2170 removed outlier: 3.678A pdb=" N LYS A2166 " --> pdb=" O GLU A2162 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA A2170 " --> pdb=" O LYS A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2173 through 2184 removed outlier: 4.294A pdb=" N TRP A2177 " --> pdb=" O GLN A2173 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET A2178 " --> pdb=" O GLN A2174 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET A2179 " --> pdb=" O ALA A2175 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A2180 " --> pdb=" O MET A2176 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A2181 " --> pdb=" O TRP A2177 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL A2182 " --> pdb=" O MET A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2187 through 2203 removed outlier: 3.822A pdb=" N GLU A2196 " --> pdb=" O ASN A2192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A2201 " --> pdb=" O ILE A2197 " (cutoff:3.500A) Processing helix chain 'A' and resid 2204 through 2207 removed outlier: 7.183A pdb=" N SER A2207 " --> pdb=" O MET A2204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2204 through 2207' Processing helix chain 'A' and resid 2208 through 2228 removed outlier: 3.730A pdb=" N THR A2216 " --> pdb=" O VAL A2212 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A2221 " --> pdb=" O ARG A2217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A2224 " --> pdb=" O ASP A2220 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS A2226 " --> pdb=" O LEU A2222 " (cutoff:3.500A) Processing helix chain 'A' and resid 2245 through 2249 Processing helix chain 'A' and resid 2249 through 2254 Processing helix chain 'A' and resid 2332 through 2352 removed outlier: 3.805A pdb=" N ARG A2337 " --> pdb=" O ARG A2333 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A2338 " --> pdb=" O LYS A2334 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A2343 " --> pdb=" O MET A2339 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2385 through 2397 removed outlier: 4.403A pdb=" N LEU A2393 " --> pdb=" O ILE A2389 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR A2394 " --> pdb=" O LEU A2390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2416 through 2429 removed outlier: 3.999A pdb=" N LEU A2429 " --> pdb=" O ARG A2425 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2443 Processing helix chain 'A' and resid 2448 through 2471 removed outlier: 3.517A pdb=" N SER A2453 " --> pdb=" O SER A2449 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A2459 " --> pdb=" O SER A2455 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A2463 " --> pdb=" O ARG A2459 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET A2464 " --> pdb=" O SER A2460 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2505 Processing helix chain 'A' and resid 2516 through 2523 removed outlier: 4.364A pdb=" N MET A2523 " --> pdb=" O MET A2519 " (cutoff:3.500A) Processing helix chain 'A' and resid 2530 through 2546 removed outlier: 3.939A pdb=" N ARG A2534 " --> pdb=" O GLY A2530 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A2538 " --> pdb=" O ARG A2534 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A2539 " --> pdb=" O ALA A2535 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A2540 " --> pdb=" O CYS A2536 " (cutoff:3.500A) Processing helix chain 'A' and resid 2547 through 2552 removed outlier: 3.907A pdb=" N SER A2552 " --> pdb=" O GLU A2548 " (cutoff:3.500A) Processing helix chain 'A' and resid 2552 through 2559 Processing helix chain 'A' and resid 2587 through 2597 removed outlier: 3.651A pdb=" N LEU A2593 " --> pdb=" O LYS A2589 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A2596 " --> pdb=" O VAL A2592 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2626 removed outlier: 4.325A pdb=" N HIS A2621 " --> pdb=" O GLU A2617 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A2622 " --> pdb=" O GLY A2618 " (cutoff:3.500A) Processing helix chain 'A' and resid 2629 through 2634 Processing helix chain 'A' and resid 2635 through 2636 No H-bonds generated for 'chain 'A' and resid 2635 through 2636' Processing helix chain 'A' and resid 2637 through 2641 Processing helix chain 'B' and resid 3 through 17 removed outlier: 4.230A pdb=" N SER B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 11 " --> pdb=" O GLU B 7 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 12 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Proline residue: B 13 - end of helix Processing helix chain 'B' and resid 26 through 44 Proline residue: B 33 - end of helix removed outlier: 3.869A pdb=" N ILE B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 43 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 44 " --> pdb=" O PHE B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 71 removed outlier: 3.641A pdb=" N ASP B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Proline residue: B 63 - end of helix Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.531A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 120 removed outlier: 3.598A pdb=" N THR B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 4.422A pdb=" N LEU B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 removed outlier: 3.537A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Proline residue: B 139 - end of helix Processing helix chain 'B' and resid 146 through 153 removed outlier: 4.976A pdb=" N GLN B 151 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 153 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 170 through 188 removed outlier: 3.892A pdb=" N MET B 175 " --> pdb=" O TRP B 171 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 176 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 179 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.574A pdb=" N ILE B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'B' and resid 235 through 250 Proline residue: B 242 - end of helix Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 262 through 279 removed outlier: 3.700A pdb=" N THR B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 277 " --> pdb=" O PHE B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 303 Proline residue: B 294 - end of helix Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 337 through 355 removed outlier: 4.281A pdb=" N GLN B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 383 removed outlier: 3.610A pdb=" N CYS B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 396 removed outlier: 3.513A pdb=" N LEU B 396 " --> pdb=" O LEU B 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 393 through 396' Processing helix chain 'B' and resid 397 through 416 removed outlier: 3.875A pdb=" N MET B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 Proline residue: B 429 - end of helix Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 446 through 459 removed outlier: 3.569A pdb=" N GLU B 450 " --> pdb=" O LYS B 446 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N HIS B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.654A pdb=" N ILE B 475 " --> pdb=" O GLU B 471 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 478 " --> pdb=" O GLN B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 483 through 500 removed outlier: 3.623A pdb=" N THR B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 516 Processing helix chain 'B' and resid 521 through 536 removed outlier: 3.561A pdb=" N LYS B 527 " --> pdb=" O LYS B 523 " (cutoff:3.500A) Proline residue: B 528 - end of helix removed outlier: 3.951A pdb=" N THR B 533 " --> pdb=" O SER B 529 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TRP B 534 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 536 " --> pdb=" O ILE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 558 removed outlier: 3.675A pdb=" N SER B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 572 removed outlier: 3.865A pdb=" N VAL B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.505A pdb=" N ASP B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 590 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS B 591 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 596 " --> pdb=" O GLY B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 613 removed outlier: 3.715A pdb=" N HIS B 602 " --> pdb=" O TRP B 598 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 635 Proline residue: B 630 - end of helix Processing helix chain 'B' and resid 641 through 653 removed outlier: 4.704A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B 647 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP B 651 " --> pdb=" O ILE B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 678 removed outlier: 3.535A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 696 removed outlier: 3.863A pdb=" N CYS B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) Proline residue: B 689 - end of helix Processing helix chain 'B' and resid 700 through 720 Processing helix chain 'B' and resid 723 through 739 removed outlier: 3.922A pdb=" N THR B 729 " --> pdb=" O THR B 725 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Proline residue: B 731 - end of helix Processing helix chain 'B' and resid 749 through 764 Processing helix chain 'B' and resid 775 through 788 removed outlier: 3.695A pdb=" N ASP B 784 " --> pdb=" O LEU B 780 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.683A pdb=" N ARG B 796 " --> pdb=" O HIS B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 808 removed outlier: 3.682A pdb=" N LYS B 803 " --> pdb=" O GLU B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 826 removed outlier: 4.470A pdb=" N ALA B 823 " --> pdb=" O ASP B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 841 through 846 Processing helix chain 'B' and resid 849 through 866 removed outlier: 4.402A pdb=" N ALA B 853 " --> pdb=" O ARG B 849 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR B 854 " --> pdb=" O MET B 850 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR B 855 " --> pdb=" O LYS B 851 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 885 Processing helix chain 'B' and resid 889 through 901 removed outlier: 3.618A pdb=" N CYS B 895 " --> pdb=" O HIS B 891 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 897 " --> pdb=" O LEU B 893 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 898 " --> pdb=" O HIS B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 931 removed outlier: 3.559A pdb=" N LYS B 930 " --> pdb=" O PHE B 926 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS B 931 " --> pdb=" O SER B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 949 removed outlier: 3.728A pdb=" N VAL B 938 " --> pdb=" O CYS B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 968 removed outlier: 3.573A pdb=" N LYS B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 991 Proline residue: B 985 - end of helix Processing helix chain 'B' and resid 999 through 1011 removed outlier: 3.845A pdb=" N ALA B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Proline residue: B1008 - end of helix removed outlier: 3.958A pdb=" N SER B1011 " --> pdb=" O SER B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1031 removed outlier: 3.561A pdb=" N LEU B1029 " --> pdb=" O ARG B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 4.274A pdb=" N SER B1043 " --> pdb=" O LEU B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1066 Processing helix chain 'B' and resid 1103 through 1115 Proline residue: B1110 - end of helix Processing helix chain 'B' and resid 1122 through 1136 removed outlier: 3.783A pdb=" N PHE B1133 " --> pdb=" O GLY B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1163 Processing helix chain 'B' and resid 1168 through 1175 removed outlier: 4.075A pdb=" N LYS B1173 " --> pdb=" O SER B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1175 through 1180 removed outlier: 3.642A pdb=" N ARG B1179 " --> pdb=" O MET B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1398 removed outlier: 3.837A pdb=" N GLU B1388 " --> pdb=" O VAL B1384 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B1392 " --> pdb=" O GLU B1388 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B1393 " --> pdb=" O ASP B1389 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B1397 " --> pdb=" O ALA B1393 " (cutoff:3.500A) Processing helix chain 'B' and resid 1401 through 1414 removed outlier: 3.977A pdb=" N ALA B1408 " --> pdb=" O TYR B1404 " (cutoff:3.500A) Processing helix chain 'B' and resid 1415 through 1417 No H-bonds generated for 'chain 'B' and resid 1415 through 1417' Processing helix chain 'B' and resid 1420 through 1433 removed outlier: 4.652A pdb=" N ILE B1427 " --> pdb=" O GLU B1423 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR B1428 " --> pdb=" O LEU B1424 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1443 Processing helix chain 'B' and resid 1446 through 1455 Processing helix chain 'B' and resid 1471 through 1479 Proline residue: B1477 - end of helix Processing helix chain 'B' and resid 1486 through 1499 Processing helix chain 'B' and resid 1503 through 1520 removed outlier: 3.765A pdb=" N ALA B1507 " --> pdb=" O ARG B1503 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B1508 " --> pdb=" O HIS B1504 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS B1509 " --> pdb=" O ASP B1505 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B1519 " --> pdb=" O SER B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1521 through 1527 removed outlier: 3.590A pdb=" N ILE B1526 " --> pdb=" O PHE B1522 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B1527 " --> pdb=" O LYS B1523 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1537 Processing helix chain 'B' and resid 1541 through 1543 No H-bonds generated for 'chain 'B' and resid 1541 through 1543' Processing helix chain 'B' and resid 1544 through 1558 removed outlier: 3.576A pdb=" N ILE B1552 " --> pdb=" O VAL B1548 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B1554 " --> pdb=" O ALA B1550 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B1556 " --> pdb=" O ILE B1552 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B1558 " --> pdb=" O ALA B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1573 through 1601 removed outlier: 3.501A pdb=" N GLN B1579 " --> pdb=" O GLN B1575 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR B1580 " --> pdb=" O LEU B1576 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B1581 " --> pdb=" O SER B1577 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B1585 " --> pdb=" O VAL B1581 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B1590 " --> pdb=" O ASP B1586 " (cutoff:3.500A) Processing helix chain 'B' and resid 1616 through 1634 Processing helix chain 'B' and resid 1638 through 1648 removed outlier: 3.515A pdb=" N ALA B1644 " --> pdb=" O THR B1640 " (cutoff:3.500A) Processing helix chain 'B' and resid 1652 through 1664 removed outlier: 3.582A pdb=" N GLU B1659 " --> pdb=" O VAL B1655 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B1660 " --> pdb=" O MET B1656 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B1663 " --> pdb=" O GLU B1659 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU B1664 " --> pdb=" O SER B1660 " (cutoff:3.500A) Processing helix chain 'B' and resid 1674 through 1683 removed outlier: 4.198A pdb=" N LYS B1678 " --> pdb=" O GLY B1674 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B1679 " --> pdb=" O PHE B1675 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET B1683 " --> pdb=" O LEU B1679 " (cutoff:3.500A) Processing helix chain 'B' and resid 1685 through 1694 removed outlier: 3.806A pdb=" N VAL B1689 " --> pdb=" O GLU B1685 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B1690 " --> pdb=" O PRO B1686 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B1693 " --> pdb=" O VAL B1689 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1694 " --> pdb=" O ALA B1690 " (cutoff:3.500A) Processing helix chain 'B' and resid 1701 through 1708 Processing helix chain 'B' and resid 1708 through 1713 removed outlier: 3.835A pdb=" N GLY B1713 " --> pdb=" O HIS B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1717 through 1729 Processing helix chain 'B' and resid 1733 through 1746 removed outlier: 3.585A pdb=" N VAL B1740 " --> pdb=" O TYR B1736 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B1741 " --> pdb=" O HIS B1737 " (cutoff:3.500A) Processing helix chain 'B' and resid 1748 through 1761 removed outlier: 4.595A pdb=" N ASN B1757 " --> pdb=" O ILE B1753 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY B1758 " --> pdb=" O THR B1754 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL B1759 " --> pdb=" O GLN B1755 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS B1760 " --> pdb=" O VAL B1756 " (cutoff:3.500A) Processing helix chain 'B' and resid 1769 through 1774 Processing helix chain 'B' and resid 1776 through 1780 Processing helix chain 'B' and resid 1784 through 1791 removed outlier: 3.537A pdb=" N LEU B1791 " --> pdb=" O VAL B1787 " (cutoff:3.500A) Processing helix chain 'B' and resid 1801 through 1813 removed outlier: 3.982A pdb=" N LEU B1808 " --> pdb=" O LEU B1804 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B1809 " --> pdb=" O GLY B1805 " (cutoff:3.500A) Processing helix chain 'B' and resid 1815 through 1827 removed outlier: 3.640A pdb=" N VAL B1826 " --> pdb=" O SER B1822 " (cutoff:3.500A) Processing helix chain 'B' and resid 1842 through 1847 removed outlier: 4.240A pdb=" N GLY B1847 " --> pdb=" O SER B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1847 through 1865 removed outlier: 4.168A pdb=" N LEU B1857 " --> pdb=" O ARG B1853 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS B1858 " --> pdb=" O LEU B1854 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1859 " --> pdb=" O HIS B1855 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B1863 " --> pdb=" O GLU B1859 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS B1865 " --> pdb=" O GLU B1861 " (cutoff:3.500A) Processing helix chain 'B' and resid 1866 through 1868 No H-bonds generated for 'chain 'B' and resid 1866 through 1868' Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.721A pdb=" N ARG B1895 " --> pdb=" O ASN B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1904 through 1913 removed outlier: 4.620A pdb=" N LEU B1910 " --> pdb=" O ALA B1906 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B1913 " --> pdb=" O SER B1909 " (cutoff:3.500A) Processing helix chain 'B' and resid 1913 through 1918 Processing helix chain 'B' and resid 1922 through 1939 removed outlier: 3.873A pdb=" N GLN B1926 " --> pdb=" O GLU B1922 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B1928 " --> pdb=" O TRP B1924 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B1933 " --> pdb=" O ARG B1929 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B1935 " --> pdb=" O ALA B1931 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1945 No H-bonds generated for 'chain 'B' and resid 1943 through 1945' Processing helix chain 'B' and resid 1946 through 1951 removed outlier: 3.546A pdb=" N SER B1950 " --> pdb=" O ASN B1946 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1973 removed outlier: 3.665A pdb=" N ASP B1968 " --> pdb=" O TRP B1964 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS B1970 " --> pdb=" O LYS B1966 " (cutoff:3.500A) Processing helix chain 'B' and resid 1975 through 1983 Processing helix chain 'B' and resid 1997 through 2005 removed outlier: 3.778A pdb=" N MET B2003 " --> pdb=" O HIS B1999 " (cutoff:3.500A) Processing helix chain 'B' and resid 2011 through 2016 removed outlier: 3.807A pdb=" N ALA B2014 " --> pdb=" O GLU B2011 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN B2015 " --> pdb=" O GLU B2012 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2032 removed outlier: 3.979A pdb=" N TYR B2025 " --> pdb=" O ILE B2021 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B2030 " --> pdb=" O LYS B2026 " (cutoff:3.500A) Processing helix chain 'B' and resid 2042 through 2057 removed outlier: 3.915A pdb=" N TYR B2046 " --> pdb=" O LEU B2042 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET B2050 " --> pdb=" O TYR B2046 " (cutoff:3.500A) Proline residue: B2051 - end of helix removed outlier: 3.791A pdb=" N ASN B2056 " --> pdb=" O MET B2052 " (cutoff:3.500A) Processing helix chain 'B' and resid 2064 through 2078 removed outlier: 3.929A pdb=" N ILE B2068 " --> pdb=" O LEU B2064 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS B2071 " --> pdb=" O TYR B2067 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N PHE B2072 " --> pdb=" O ILE B2068 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY B2073 " --> pdb=" O VAL B2069 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B2074 " --> pdb=" O LEU B2070 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B2076 " --> pdb=" O PHE B2072 " (cutoff:3.500A) Processing helix chain 'B' and resid 2086 through 2100 removed outlier: 3.527A pdb=" N MET B2090 " --> pdb=" O SER B2086 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B2099 " --> pdb=" O LEU B2095 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 2101 through 2109 Processing helix chain 'B' and resid 2111 through 2133 removed outlier: 4.170A pdb=" N MET B2115 " --> pdb=" O ASP B2111 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN B2117 " --> pdb=" O VAL B2113 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B2125 " --> pdb=" O LYS B2121 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B2127 " --> pdb=" O ASN B2123 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B2128 " --> pdb=" O LYS B2124 " (cutoff:3.500A) Processing helix chain 'B' and resid 2134 through 2139 Processing helix chain 'B' and resid 2141 through 2148 Processing helix chain 'B' and resid 2153 through 2169 removed outlier: 3.533A pdb=" N ALA B2165 " --> pdb=" O MET B2161 " (cutoff:3.500A) Processing helix chain 'B' and resid 2171 through 2184 removed outlier: 3.977A pdb=" N ALA B2175 " --> pdb=" O TYR B2171 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B2178 " --> pdb=" O GLN B2174 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B2180 " --> pdb=" O MET B2176 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA B2181 " --> pdb=" O TRP B2177 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B2182 " --> pdb=" O MET B2178 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS B2184 " --> pdb=" O THR B2180 " (cutoff:3.500A) Processing helix chain 'B' and resid 2187 through 2203 removed outlier: 3.598A pdb=" N ARG B2193 " --> pdb=" O MET B2189 " (cutoff:3.500A) Processing helix chain 'B' and resid 2208 through 2228 removed outlier: 3.708A pdb=" N VAL B2212 " --> pdb=" O LEU B2208 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B2213 " --> pdb=" O GLU B2209 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS B2226 " --> pdb=" O LEU B2222 " (cutoff:3.500A) Processing helix chain 'B' and resid 2245 through 2249 Processing helix chain 'B' and resid 2249 through 2254 removed outlier: 3.783A pdb=" N ALA B2253 " --> pdb=" O LEU B2249 " (cutoff:3.500A) Processing helix chain 'B' and resid 2332 through 2352 removed outlier: 3.872A pdb=" N ARG B2337 " --> pdb=" O ARG B2333 " (cutoff:3.500A) Processing helix chain 'B' and resid 2352 through 2358 removed outlier: 4.278A pdb=" N ARG B2356 " --> pdb=" O ASP B2352 " (cutoff:3.500A) Processing helix chain 'B' and resid 2385 through 2395 Processing helix chain 'B' and resid 2416 through 2426 Processing helix chain 'B' and resid 2434 through 2443 removed outlier: 4.199A pdb=" N LEU B2441 " --> pdb=" O HIS B2437 " (cutoff:3.500A) Processing helix chain 'B' and resid 2450 through 2472 removed outlier: 4.179A pdb=" N ARG B2459 " --> pdb=" O SER B2455 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B2461 " --> pdb=" O TYR B2457 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL B2463 " --> pdb=" O ARG B2459 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET B2464 " --> pdb=" O SER B2460 " (cutoff:3.500A) Processing helix chain 'B' and resid 2516 through 2522 Processing helix chain 'B' and resid 2530 through 2546 removed outlier: 3.606A pdb=" N VAL B2538 " --> pdb=" O ARG B2534 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B2540 " --> pdb=" O CYS B2536 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B2546 " --> pdb=" O LEU B2542 " (cutoff:3.500A) Processing helix chain 'B' and resid 2546 through 2559 removed outlier: 3.655A pdb=" N LEU B2550 " --> pdb=" O GLN B2546 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B2552 " --> pdb=" O GLU B2548 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B2553 " --> pdb=" O PRO B2549 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B2554 " --> pdb=" O LEU B2550 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS B2555 " --> pdb=" O MET B2551 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR B2556 " --> pdb=" O SER B2552 " (cutoff:3.500A) Processing helix chain 'B' and resid 2587 through 2599 removed outlier: 3.664A pdb=" N GLU B2596 " --> pdb=" O VAL B2592 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B2598 " --> pdb=" O ASP B2594 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2629 removed outlier: 3.848A pdb=" N LEU B2623 " --> pdb=" O HIS B2619 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN B2625 " --> pdb=" O HIS B2621 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B2627 " --> pdb=" O LEU B2623 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B2628 " --> pdb=" O ILE B2624 " (cutoff:3.500A) Processing helix chain 'B' and resid 2629 through 2635 removed outlier: 3.609A pdb=" N CYS B2634 " --> pdb=" O GLU B2630 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN B2635 " --> pdb=" O ASN B2631 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 29 through 42 Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.517A pdb=" N ASP C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Proline residue: C 48 - end of helix Processing helix chain 'C' and resid 65 through 74 removed outlier: 3.659A pdb=" N LEU C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 100 removed outlier: 4.211A pdb=" N VAL C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N HIS C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 89 " --> pdb=" O HIS C 85 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.511A pdb=" N LEU C 114 " --> pdb=" O ASP C 110 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS C 122 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.644A pdb=" N LEU C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 160 removed outlier: 3.589A pdb=" N LEU C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 159 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 176 through 180 removed outlier: 4.109A pdb=" N LYS C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.578A pdb=" N ASN C 213 " --> pdb=" O SER C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 231 Proline residue: C 225 - end of helix Proline residue: C 229 - end of helix Processing helix chain 'C' and resid 237 through 251 Proline residue: C 248 - end of helix removed outlier: 3.565A pdb=" N GLU C 251 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.565A pdb=" N GLY C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 297 through 319 removed outlier: 3.574A pdb=" N ARG C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 346 Proline residue: C 340 - end of helix Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 350 through 361 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.570A pdb=" N ARG D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 74 removed outlier: 3.599A pdb=" N GLN D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 removed outlier: 4.356A pdb=" N HIS D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 107 through 122 removed outlier: 3.712A pdb=" N LYS D 122 " --> pdb=" O GLN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.595A pdb=" N VAL D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU D 133 " --> pdb=" O LYS D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 removed outlier: 3.530A pdb=" N SER D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.644A pdb=" N PHE D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.638A pdb=" N ALA D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 228 Proline residue: D 225 - end of helix Processing helix chain 'D' and resid 238 through 255 Proline residue: D 248 - end of helix Processing helix chain 'D' and resid 268 through 279 removed outlier: 4.398A pdb=" N GLY D 274 " --> pdb=" O LYS D 270 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 removed outlier: 4.253A pdb=" N LEU D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 279 through 284' Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.632A pdb=" N ILE D 311 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2243 through 2244 removed outlier: 7.348A pdb=" N MET A2299 " --> pdb=" O SER A2313 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N SER A2313 " --> pdb=" O MET A2299 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A2310 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N CYS A2326 " --> pdb=" O LYS A2310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2481 through 2483 Processing sheet with id=AA3, first strand: chain 'B' and resid 2243 through 2244 removed outlier: 7.433A pdb=" N MET B2299 " --> pdb=" O SER B2313 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER B2313 " --> pdb=" O MET B2299 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B2310 " --> pdb=" O CYS B2326 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS B2326 " --> pdb=" O LYS B2310 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B2323 " --> pdb=" O TRP B2379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2481 through 2483 2089 hydrogen bonds defined for protein. 6177 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: 17.03 Time building geometry restraints manager: 15.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11889 1.34 - 1.46: 7405 1.46 - 1.59: 14235 1.59 - 1.71: 0 1.71 - 1.84: 208 Bond restraints: 33737 Sorted by residual: bond pdb=" C THR A2641 " pdb=" O THR A2641 " ideal model delta sigma weight residual 1.235 1.261 -0.026 4.70e-03 4.53e+04 3.04e+01 bond pdb=" CB ASN B2080 " pdb=" CG ASN B2080 " ideal model delta sigma weight residual 1.516 1.435 0.081 2.50e-02 1.60e+03 1.05e+01 bond pdb=" C LYS B2308 " pdb=" N PRO B2309 " ideal model delta sigma weight residual 1.329 1.367 -0.038 1.20e-02 6.94e+03 9.99e+00 bond pdb=" CA ALA A2020 " pdb=" CB ALA A2020 " ideal model delta sigma weight residual 1.530 1.485 0.045 1.48e-02 4.57e+03 9.31e+00 bond pdb=" CB TRP B1779 " pdb=" CG TRP B1779 " ideal model delta sigma weight residual 1.498 1.410 0.088 3.10e-02 1.04e+03 8.03e+00 ... (remaining 33732 not shown) Histogram of bond angle deviations from ideal: 97.52 - 105.01: 364 105.01 - 112.51: 17999 112.51 - 120.00: 12767 120.00 - 127.49: 14845 127.49 - 134.98: 301 Bond angle restraints: 46276 Sorted by residual: angle pdb=" N PRO D 24 " pdb=" CA PRO D 24 " pdb=" CB PRO D 24 " ideal model delta sigma weight residual 102.81 109.85 -7.04 6.70e-01 2.23e+00 1.10e+02 angle pdb=" N PRO D 235 " pdb=" CA PRO D 235 " pdb=" CB PRO D 235 " ideal model delta sigma weight residual 101.88 111.00 -9.12 1.01e+00 9.80e-01 8.16e+01 angle pdb=" N PRO A 358 " pdb=" CA PRO A 358 " pdb=" CB PRO A 358 " ideal model delta sigma weight residual 103.25 111.99 -8.74 1.05e+00 9.07e-01 6.93e+01 angle pdb=" N PRO A1189 " pdb=" CA PRO A1189 " pdb=" CB PRO A1189 " ideal model delta sigma weight residual 103.25 111.88 -8.63 1.05e+00 9.07e-01 6.75e+01 angle pdb=" N PRO D 107 " pdb=" CA PRO D 107 " pdb=" CB PRO D 107 " ideal model delta sigma weight residual 103.25 111.85 -8.60 1.05e+00 9.07e-01 6.70e+01 ... (remaining 46271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.96: 18721 14.96 - 29.92: 1225 29.92 - 44.87: 156 44.87 - 59.83: 35 59.83 - 74.79: 7 Dihedral angle restraints: 20144 sinusoidal: 4350 harmonic: 15794 Sorted by residual: dihedral pdb=" CA GLU A2564 " pdb=" C GLU A2564 " pdb=" N TRP A2565 " pdb=" CA TRP A2565 " ideal model delta harmonic sigma weight residual -180.00 -107.52 -72.48 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CA ARG A1846 " pdb=" C ARG A1846 " pdb=" N GLY A1847 " pdb=" CA GLY A1847 " ideal model delta harmonic sigma weight residual 180.00 111.61 68.39 0 5.00e+00 4.00e-02 1.87e+02 dihedral pdb=" CA ARG B1846 " pdb=" C ARG B1846 " pdb=" N GLY B1847 " pdb=" CA GLY B1847 " ideal model delta harmonic sigma weight residual 180.00 116.38 63.62 0 5.00e+00 4.00e-02 1.62e+02 ... (remaining 20141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4827 0.078 - 0.156: 700 0.156 - 0.234: 119 0.234 - 0.312: 97 0.312 - 0.390: 10 Chirality restraints: 5753 Sorted by residual: chirality pdb=" CA PRO B 445 " pdb=" N PRO B 445 " pdb=" C PRO B 445 " pdb=" CB PRO B 445 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA PRO A 445 " pdb=" N PRO A 445 " pdb=" C PRO A 445 " pdb=" CB PRO A 445 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CG LEU A2076 " pdb=" CB LEU A2076 " pdb=" CD1 LEU A2076 " pdb=" CD2 LEU A2076 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 5750 not shown) Planarity restraints: 6264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B1984 " -0.087 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO B1985 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO B1985 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO B1985 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1984 " 0.086 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A1985 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A1985 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A1985 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1776 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C GLU B1776 " 0.082 2.00e-02 2.50e+03 pdb=" O GLU B1776 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA B1777 " -0.028 2.00e-02 2.50e+03 ... (remaining 6261 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1574 2.70 - 3.25: 37924 3.25 - 3.80: 56917 3.80 - 4.35: 70489 4.35 - 4.90: 96294 Nonbonded interactions: 263198 Sorted by model distance: nonbonded pdb=" O PHE B1184 " pdb=" OH TYR B1844 " model vdw 2.154 2.440 nonbonded pdb=" O PHE A1184 " pdb=" OH TYR A1844 " model vdw 2.195 2.440 nonbonded pdb=" O LYS B2587 " pdb=" OG1 THR B2590 " model vdw 2.214 2.440 nonbonded pdb=" O ALA B1642 " pdb=" OG SER B1645 " model vdw 2.222 2.440 nonbonded pdb=" O LYS A2587 " pdb=" OG1 THR A2590 " model vdw 2.224 2.440 ... (remaining 263193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 5 through 322) selection = chain 'D' } 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 4.910 Check model and map are aligned: 0.530 Set scattering table: 0.310 Process input model: 98.140 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.240 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.008 0.088 33737 Z= 0.531 Angle : 1.371 14.768 46276 Z= 0.860 Chirality : 0.069 0.390 5753 Planarity : 0.007 0.132 6264 Dihedral : 11.419 74.788 9812 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 1.68 % Allowed : 15.57 % Favored : 82.76 % Rotamer: Outliers : 0.97 % Allowed : 3.30 % Favored : 95.73 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.47 % Twisted Proline : 7.30 % Twisted General : 1.86 % 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: -4.74 (0.09), residues: 5364 helix: -3.23 (0.06), residues: 2599 sheet: -3.15 (0.65), residues: 56 loop : -3.07 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP B2104 HIS 0.024 0.005 HIS B2492 PHE 0.050 0.003 PHE A2436 TYR 0.050 0.004 TYR B1535 ARG 0.018 0.002 ARG A1774 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 640 time to evaluate : 4.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1582 PHE cc_start: 0.9433 (m-80) cc_final: 0.9073 (m-80) REVERT: A 1587 HIS cc_start: 0.9264 (m-70) cc_final: 0.8905 (m90) REVERT: A 1653 ARG cc_start: 0.9367 (mtt180) cc_final: 0.9106 (ttm-80) REVERT: A 1656 MET cc_start: 0.8653 (tpt) cc_final: 0.8409 (tpt) REVERT: A 1740 VAL cc_start: 0.9577 (t) cc_final: 0.9282 (p) REVERT: A 2010 MET cc_start: 0.9458 (mmm) cc_final: 0.8911 (mmm) REVERT: A 2019 ASN cc_start: 0.8365 (m-40) cc_final: 0.7715 (m-40) REVERT: A 2091 LEU cc_start: 0.9452 (mt) cc_final: 0.9090 (mt) REVERT: A 2093 LEU cc_start: 0.9375 (mt) cc_final: 0.8852 (mt) REVERT: A 2097 TYR cc_start: 0.7970 (m-80) cc_final: 0.7677 (m-80) REVERT: A 2144 GLN cc_start: 0.9210 (mt0) cc_final: 0.8918 (mp10) REVERT: A 2162 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8634 (pp20) REVERT: A 2166 LYS cc_start: 0.9313 (mttt) cc_final: 0.8826 (ptmm) REVERT: A 2310 LYS cc_start: 0.9305 (mtmt) cc_final: 0.8755 (mppt) REVERT: A 2423 VAL cc_start: 0.9371 (t) cc_final: 0.9033 (p) REVERT: A 2436 PHE cc_start: 0.8549 (m-80) cc_final: 0.7966 (m-80) REVERT: A 2437 HIS cc_start: 0.8661 (t70) cc_final: 0.8296 (t70) REVERT: A 2464 MET cc_start: 0.8504 (tpt) cc_final: 0.8244 (tpt) REVERT: A 2489 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 2515 LEU cc_start: 0.9544 (tp) cc_final: 0.9339 (tp) REVERT: A 2523 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.7186 (pp-130) REVERT: A 2531 LEU cc_start: 0.9675 (mt) cc_final: 0.9442 (mt) REVERT: A 2534 ARG cc_start: 0.9023 (tpt170) cc_final: 0.8687 (tpp80) REVERT: A 2554 LEU cc_start: 0.9392 (mt) cc_final: 0.9161 (mt) REVERT: A 2595 ILE cc_start: 0.9762 (mt) cc_final: 0.9491 (mm) REVERT: A 2632 LEU cc_start: 0.9292 (tm) cc_final: 0.8672 (tt) REVERT: B 1575 GLN cc_start: 0.8778 (mt0) cc_final: 0.8346 (mp10) REVERT: B 1582 PHE cc_start: 0.9249 (m-80) cc_final: 0.8844 (m-80) REVERT: B 1584 MET cc_start: 0.8901 (mtm) cc_final: 0.8405 (mmp) REVERT: B 1702 LEU cc_start: 0.9081 (mt) cc_final: 0.8651 (tt) REVERT: B 1703 LYS cc_start: 0.9367 (mttt) cc_final: 0.8890 (ptpt) REVERT: B 1742 SER cc_start: 0.9762 (m) cc_final: 0.9540 (p) REVERT: B 1743 MET cc_start: 0.9453 (mmm) cc_final: 0.8849 (mmm) REVERT: B 1749 LEU cc_start: 0.9577 (mt) cc_final: 0.9020 (mt) REVERT: B 1826 VAL cc_start: 0.9524 (OUTLIER) cc_final: 0.9180 (p) REVERT: B 1889 MET cc_start: 0.7841 (mmm) cc_final: 0.7362 (mmm) REVERT: B 1901 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8243 (tm) REVERT: B 1942 ASN cc_start: 0.8955 (m-40) cc_final: 0.8578 (p0) REVERT: B 1951 ARG cc_start: 0.7191 (mpp80) cc_final: 0.6726 (ttp-110) REVERT: B 2010 MET cc_start: 0.8729 (mmm) cc_final: 0.8505 (mmm) REVERT: B 2024 LYS cc_start: 0.9220 (mttt) cc_final: 0.8948 (tttm) REVERT: B 2040 PHE cc_start: 0.7580 (p90) cc_final: 0.7288 (p90) REVERT: B 2052 MET cc_start: 0.9223 (mmm) cc_final: 0.8848 (mmp) REVERT: B 2069 VAL cc_start: 0.9537 (t) cc_final: 0.9256 (m) REVERT: B 2074 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7569 (mtp85) REVERT: B 2084 TYR cc_start: 0.7684 (t80) cc_final: 0.7426 (t80) REVERT: B 2094 TRP cc_start: 0.8079 (m100) cc_final: 0.7555 (m100) REVERT: B 2129 HIS cc_start: 0.8543 (t70) cc_final: 0.8178 (t-170) REVERT: B 2132 TYR cc_start: 0.9031 (m-80) cc_final: 0.8477 (m-80) REVERT: B 2140 THR cc_start: 0.8842 (p) cc_final: 0.8633 (p) REVERT: B 2206 LYS cc_start: 0.9062 (mttt) cc_final: 0.8669 (ptpp) REVERT: B 2324 MET cc_start: 0.9446 (mmm) cc_final: 0.8943 (mmm) REVERT: B 2338 LEU cc_start: 0.9662 (mt) cc_final: 0.9334 (mt) REVERT: B 2347 LYS cc_start: 0.9405 (mttt) cc_final: 0.8905 (mmmt) REVERT: B 2349 LEU cc_start: 0.9698 (mt) cc_final: 0.9340 (mp) REVERT: B 2356 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7443 (mmm160) REVERT: B 2376 ILE cc_start: 0.9044 (mt) cc_final: 0.8505 (mm) REVERT: B 2407 ARG cc_start: 0.8825 (mtt180) cc_final: 0.8599 (tpt90) REVERT: B 2438 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8717 (mt-10) REVERT: B 2531 LEU cc_start: 0.9068 (mt) cc_final: 0.8840 (tt) REVERT: B 2593 LEU cc_start: 0.9461 (mt) cc_final: 0.9035 (mm) REVERT: B 2597 GLN cc_start: 0.9174 (mp10) cc_final: 0.8950 (mp10) REVERT: B 2629 ASP cc_start: 0.7684 (m-30) cc_final: 0.7465 (m-30) outliers start: 18 outliers final: 2 residues processed: 653 average time/residue: 0.5152 time to fit residues: 523.4470 Evaluate side-chains 453 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 448 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 455 optimal weight: 0.9990 chunk 408 optimal weight: 7.9990 chunk 226 optimal weight: 0.8980 chunk 139 optimal weight: 20.0000 chunk 275 optimal weight: 0.0050 chunk 218 optimal weight: 0.8980 chunk 422 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 256 optimal weight: 0.4980 chunk 314 optimal weight: 6.9990 chunk 489 optimal weight: 5.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1672 HIS A1748 GLN A1755 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 HIS A1937 HIS A1971 GLN A2019 ASN ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2117 ASN A2123 ASN ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 ASN ** A2382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2496 ASN A2517 HIS ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1672 HIS B1748 GLN B1771 ASN B1845 GLN B1936 HIS ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1971 GLN ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 GLN B2117 ASN ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2591 HIS B2635 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 33737 Z= 0.244 Angle : 0.848 11.833 46276 Z= 0.465 Chirality : 0.046 0.271 5753 Planarity : 0.006 0.113 6264 Dihedral : 9.053 60.412 5588 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.78 % Allowed : 13.81 % Favored : 85.40 % Rotamer: Outliers : 0.43 % Allowed : 3.84 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 4.29 % Twisted General : 0.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.10), residues: 5364 helix: -1.92 (0.07), residues: 3542 sheet: -3.19 (0.61), residues: 57 loop : -3.78 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A2104 HIS 0.009 0.002 HIS A2153 PHE 0.028 0.002 PHE A2499 TYR 0.040 0.002 TYR A2394 ARG 0.009 0.001 ARG A2407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 594 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1537 LEU cc_start: 0.9352 (mt) cc_final: 0.9128 (mt) REVERT: A 1542 GLN cc_start: 0.9581 (mt0) cc_final: 0.9296 (pm20) REVERT: A 1582 PHE cc_start: 0.9213 (m-80) cc_final: 0.8691 (m-80) REVERT: A 1657 HIS cc_start: 0.8904 (m-70) cc_final: 0.8652 (m-70) REVERT: A 1665 LYS cc_start: 0.9186 (mttt) cc_final: 0.8600 (mttt) REVERT: A 1733 ILE cc_start: 0.9003 (mt) cc_final: 0.8712 (mm) REVERT: A 1743 MET cc_start: 0.9287 (mtm) cc_final: 0.9050 (ptp) REVERT: A 2010 MET cc_start: 0.9288 (mmm) cc_final: 0.8776 (mmm) REVERT: A 2022 MET cc_start: 0.8509 (mtt) cc_final: 0.8081 (mtt) REVERT: A 2026 LYS cc_start: 0.9570 (mtmm) cc_final: 0.9317 (mmmt) REVERT: A 2093 LEU cc_start: 0.9456 (mt) cc_final: 0.8802 (mt) REVERT: A 2097 TYR cc_start: 0.8205 (m-80) cc_final: 0.7839 (m-80) REVERT: A 2100 LYS cc_start: 0.9280 (mttt) cc_final: 0.9067 (mmmt) REVERT: A 2115 MET cc_start: 0.8878 (mmp) cc_final: 0.8631 (mmm) REVERT: A 2144 GLN cc_start: 0.9045 (mt0) cc_final: 0.8778 (mp10) REVERT: A 2166 LYS cc_start: 0.9027 (mttt) cc_final: 0.8769 (ptmm) REVERT: A 2231 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.6924 (p0) REVERT: A 2310 LYS cc_start: 0.9281 (mtmt) cc_final: 0.8888 (mppt) REVERT: A 2338 LEU cc_start: 0.9656 (mp) cc_final: 0.9420 (mp) REVERT: A 2339 MET cc_start: 0.9075 (mmt) cc_final: 0.8517 (mmt) REVERT: A 2372 ASP cc_start: 0.8259 (p0) cc_final: 0.8048 (p0) REVERT: A 2429 LEU cc_start: 0.9318 (mt) cc_final: 0.8876 (tp) REVERT: A 2458 CYS cc_start: 0.9570 (m) cc_final: 0.9329 (p) REVERT: A 2466 MET cc_start: 0.8894 (mmp) cc_final: 0.8158 (mmp) REVERT: A 2467 VAL cc_start: 0.9309 (t) cc_final: 0.8616 (p) REVERT: A 2489 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 2531 LEU cc_start: 0.9494 (mt) cc_final: 0.9258 (mt) REVERT: A 2539 THR cc_start: 0.9720 (p) cc_final: 0.7797 (p) REVERT: A 2540 MET cc_start: 0.8937 (mmp) cc_final: 0.7501 (mmp) REVERT: A 2557 PHE cc_start: 0.9108 (t80) cc_final: 0.8875 (t80) REVERT: B 1575 GLN cc_start: 0.8702 (mt0) cc_final: 0.8330 (mp10) REVERT: B 1582 PHE cc_start: 0.9249 (m-80) cc_final: 0.8752 (m-80) REVERT: B 1702 LEU cc_start: 0.9183 (mt) cc_final: 0.8460 (tt) REVERT: B 1703 LYS cc_start: 0.9131 (mttt) cc_final: 0.8829 (ptpt) REVERT: B 1724 ARG cc_start: 0.9313 (ptm-80) cc_final: 0.9107 (ptt90) REVERT: B 1841 ARG cc_start: 0.9017 (mmm-85) cc_final: 0.8614 (tpp80) REVERT: B 1889 MET cc_start: 0.7735 (mmm) cc_final: 0.7349 (mmm) REVERT: B 1942 ASN cc_start: 0.8696 (m-40) cc_final: 0.8432 (p0) REVERT: B 1961 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8466 (mmtt) REVERT: B 1962 TRP cc_start: 0.8135 (t60) cc_final: 0.7889 (t60) REVERT: B 1996 MET cc_start: 0.8926 (mpp) cc_final: 0.8160 (pmm) REVERT: B 2022 MET cc_start: 0.7711 (mtt) cc_final: 0.7092 (mtt) REVERT: B 2040 PHE cc_start: 0.7476 (p90) cc_final: 0.7122 (p90) REVERT: B 2052 MET cc_start: 0.9038 (mmm) cc_final: 0.8568 (mmp) REVERT: B 2055 ASP cc_start: 0.9562 (m-30) cc_final: 0.9343 (m-30) REVERT: B 2074 ARG cc_start: 0.7424 (mtt180) cc_final: 0.6951 (mtm-85) REVERT: B 2078 TYR cc_start: 0.7523 (t80) cc_final: 0.7049 (t80) REVERT: B 2087 MET cc_start: 0.8027 (tpt) cc_final: 0.7783 (tpt) REVERT: B 2094 TRP cc_start: 0.7809 (m100) cc_final: 0.7568 (m100) REVERT: B 2129 HIS cc_start: 0.8136 (t70) cc_final: 0.7843 (t70) REVERT: B 2179 MET cc_start: 0.8782 (tpp) cc_final: 0.8510 (tpp) REVERT: B 2195 LYS cc_start: 0.9537 (mttt) cc_final: 0.9301 (mmmt) REVERT: B 2206 LYS cc_start: 0.9212 (mttt) cc_final: 0.8682 (ptpp) REVERT: B 2338 LEU cc_start: 0.9449 (mt) cc_final: 0.9232 (mt) REVERT: B 2339 MET cc_start: 0.9245 (mmt) cc_final: 0.8272 (mmt) REVERT: B 2347 LYS cc_start: 0.9251 (mttt) cc_final: 0.8954 (mmmt) REVERT: B 2349 LEU cc_start: 0.9530 (mt) cc_final: 0.9261 (mp) REVERT: B 2364 THR cc_start: 0.9545 (p) cc_final: 0.8907 (p) REVERT: B 2376 ILE cc_start: 0.8801 (mt) cc_final: 0.8555 (mm) REVERT: B 2438 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8429 (mt-10) REVERT: B 2458 CYS cc_start: 0.9446 (m) cc_final: 0.9009 (p) REVERT: B 2475 ASP cc_start: 0.7763 (t0) cc_final: 0.7248 (t70) REVERT: B 2479 GLU cc_start: 0.7941 (pp20) cc_final: 0.7686 (tm-30) REVERT: B 2548 GLU cc_start: 0.9271 (mp0) cc_final: 0.8967 (mp0) REVERT: B 2594 ASP cc_start: 0.8870 (m-30) cc_final: 0.8393 (m-30) REVERT: B 2597 GLN cc_start: 0.8969 (mp10) cc_final: 0.8644 (pt0) REVERT: B 2635 GLN cc_start: 0.9126 (mt0) cc_final: 0.8551 (tm-30) REVERT: B 2644 MET cc_start: 0.7858 (mmm) cc_final: 0.7551 (mmm) outliers start: 8 outliers final: 1 residues processed: 599 average time/residue: 0.5039 time to fit residues: 484.9472 Evaluate side-chains 451 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 449 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 272 optimal weight: 30.0000 chunk 151 optimal weight: 0.0030 chunk 407 optimal weight: 1.9990 chunk 333 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 490 optimal weight: 0.0030 chunk 529 optimal weight: 2.9990 chunk 436 optimal weight: 0.9980 chunk 486 optimal weight: 50.0000 chunk 167 optimal weight: 6.9990 chunk 393 optimal weight: 0.9980 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1531 HIS ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1735 HIS A1737 HIS ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2123 ASN A2151 HIS ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2591 HIS A2597 GLN ** A2625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 33737 Z= 0.204 Angle : 0.740 10.633 46276 Z= 0.403 Chirality : 0.043 0.221 5753 Planarity : 0.005 0.106 6264 Dihedral : 8.226 56.418 5588 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.02 % Favored : 85.37 % Rotamer: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.43 % Twisted General : 0.66 % 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: -2.96 (0.11), residues: 5364 helix: -1.12 (0.08), residues: 3563 sheet: -2.62 (0.62), residues: 57 loop : -3.64 (0.15), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A2104 HIS 0.011 0.002 HIS A2151 PHE 0.037 0.002 PHE A2436 TYR 0.028 0.002 TYR B2132 ARG 0.010 0.001 ARG A1959 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 537 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 GLN cc_start: 0.9538 (mt0) cc_final: 0.9331 (pm20) REVERT: A 1582 PHE cc_start: 0.9204 (m-80) cc_final: 0.8696 (m-80) REVERT: A 1663 THR cc_start: 0.8374 (p) cc_final: 0.8067 (p) REVERT: A 1740 VAL cc_start: 0.9704 (t) cc_final: 0.9432 (p) REVERT: A 1932 ARG cc_start: 0.8538 (mtt90) cc_final: 0.8336 (mtt-85) REVERT: A 1961 LYS cc_start: 0.7747 (mttp) cc_final: 0.7495 (mptt) REVERT: A 1976 LEU cc_start: 0.9484 (mp) cc_final: 0.9248 (mt) REVERT: A 2010 MET cc_start: 0.9227 (mmm) cc_final: 0.8736 (mmm) REVERT: A 2016 PHE cc_start: 0.7433 (p90) cc_final: 0.7182 (p90) REVERT: A 2026 LYS cc_start: 0.9559 (mtmm) cc_final: 0.9281 (mmtm) REVERT: A 2050 MET cc_start: 0.9160 (mmm) cc_final: 0.8899 (mmm) REVERT: A 2058 MET cc_start: 0.8110 (ptm) cc_final: 0.7109 (ppp) REVERT: A 2074 ARG cc_start: 0.8062 (mtp85) cc_final: 0.7273 (ptm160) REVERT: A 2087 MET cc_start: 0.8171 (tpt) cc_final: 0.7950 (tpt) REVERT: A 2093 LEU cc_start: 0.9311 (mt) cc_final: 0.8794 (mt) REVERT: A 2097 TYR cc_start: 0.7870 (m-80) cc_final: 0.7505 (m-80) REVERT: A 2099 THR cc_start: 0.9322 (p) cc_final: 0.8912 (p) REVERT: A 2100 LYS cc_start: 0.9244 (mttt) cc_final: 0.8890 (mmtm) REVERT: A 2155 GLU cc_start: 0.8552 (tp30) cc_final: 0.8231 (tp30) REVERT: A 2163 ILE cc_start: 0.9463 (mt) cc_final: 0.9005 (mt) REVERT: A 2225 LEU cc_start: 0.9799 (mt) cc_final: 0.9465 (mt) REVERT: A 2310 LYS cc_start: 0.9228 (mtmt) cc_final: 0.8720 (mppt) REVERT: A 2324 MET cc_start: 0.8946 (mmm) cc_final: 0.8429 (mmm) REVERT: A 2325 MET cc_start: 0.8166 (mmp) cc_final: 0.7757 (mtp) REVERT: A 2339 MET cc_start: 0.9047 (mmt) cc_final: 0.8484 (mmt) REVERT: A 2372 ASP cc_start: 0.8203 (p0) cc_final: 0.7983 (p0) REVERT: A 2429 LEU cc_start: 0.9442 (mt) cc_final: 0.8998 (tp) REVERT: A 2437 HIS cc_start: 0.8377 (t70) cc_final: 0.7841 (t70) REVERT: A 2489 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8424 (mt-10) REVERT: A 2531 LEU cc_start: 0.9532 (mt) cc_final: 0.9303 (mt) REVERT: A 2539 THR cc_start: 0.9664 (p) cc_final: 0.9142 (p) REVERT: A 2540 MET cc_start: 0.9002 (mmp) cc_final: 0.8682 (mmm) REVERT: A 2543 MET cc_start: 0.9001 (mtm) cc_final: 0.8010 (mtm) REVERT: A 2594 ASP cc_start: 0.8130 (m-30) cc_final: 0.7903 (m-30) REVERT: A 2597 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8552 (mp10) REVERT: A 2636 MET cc_start: 0.8901 (mmp) cc_final: 0.8700 (mmm) REVERT: B 1575 GLN cc_start: 0.8707 (mt0) cc_final: 0.8305 (mp10) REVERT: B 1582 PHE cc_start: 0.9173 (m-80) cc_final: 0.8778 (m-80) REVERT: B 1651 TYR cc_start: 0.8427 (m-80) cc_final: 0.8145 (m-80) REVERT: B 1702 LEU cc_start: 0.9236 (mt) cc_final: 0.8726 (pt) REVERT: B 1703 LYS cc_start: 0.8874 (mttt) cc_final: 0.8631 (ptpt) REVERT: B 1741 LYS cc_start: 0.9331 (mmmm) cc_final: 0.8982 (mmmt) REVERT: B 1841 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8439 (tpt-90) REVERT: B 1889 MET cc_start: 0.7831 (mmm) cc_final: 0.7398 (mmm) REVERT: B 1895 ARG cc_start: 0.9118 (mpp80) cc_final: 0.8643 (ptp90) REVERT: B 1951 ARG cc_start: 0.8404 (ptt180) cc_final: 0.8099 (ptt-90) REVERT: B 1961 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8281 (mmtt) REVERT: B 1962 TRP cc_start: 0.8239 (t60) cc_final: 0.7535 (t60) REVERT: B 1996 MET cc_start: 0.8390 (mpp) cc_final: 0.8121 (pmm) REVERT: B 2003 MET cc_start: 0.8245 (mmm) cc_final: 0.7712 (tpp) REVERT: B 2040 PHE cc_start: 0.7522 (p90) cc_final: 0.7090 (p90) REVERT: B 2052 MET cc_start: 0.9046 (mmm) cc_final: 0.8632 (mmp) REVERT: B 2087 MET cc_start: 0.7706 (tpt) cc_final: 0.7453 (tpt) REVERT: B 2206 LYS cc_start: 0.9186 (mttt) cc_final: 0.8604 (ptpp) REVERT: B 2338 LEU cc_start: 0.9441 (mt) cc_final: 0.9196 (mt) REVERT: B 2339 MET cc_start: 0.9254 (mmt) cc_final: 0.8170 (mmt) REVERT: B 2356 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7466 (mtp85) REVERT: B 2376 ILE cc_start: 0.8823 (mt) cc_final: 0.8529 (mm) REVERT: B 2438 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8617 (mt-10) REVERT: B 2475 ASP cc_start: 0.7855 (t0) cc_final: 0.7459 (t70) REVERT: B 2529 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7632 (mp0) REVERT: B 2558 LEU cc_start: 0.9258 (mt) cc_final: 0.9056 (mt) REVERT: B 2594 ASP cc_start: 0.8849 (m-30) cc_final: 0.8609 (m-30) REVERT: B 2596 GLU cc_start: 0.9055 (pt0) cc_final: 0.8807 (pp20) REVERT: B 2597 GLN cc_start: 0.9038 (mp10) cc_final: 0.8536 (mt0) outliers start: 2 outliers final: 0 residues processed: 539 average time/residue: 0.4653 time to fit residues: 405.6332 Evaluate side-chains 426 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 425 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 484 optimal weight: 0.0020 chunk 368 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 54 optimal weight: 30.0000 chunk 234 optimal weight: 1.9990 chunk 329 optimal weight: 0.0170 chunk 492 optimal weight: 7.9990 chunk 521 optimal weight: 40.0000 chunk 257 optimal weight: 30.0000 chunk 466 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 overall best weight: 1.6032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1748 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2081 GLN A2123 ASN ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2263 GLN ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2585 ASN A2597 GLN ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1755 GLN ** B1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 GLN ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33737 Z= 0.202 Angle : 0.715 10.181 46276 Z= 0.390 Chirality : 0.043 0.201 5753 Planarity : 0.005 0.101 6264 Dihedral : 7.675 56.326 5588 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.98 % Favored : 85.40 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.54 % 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: -2.11 (0.11), residues: 5364 helix: -0.39 (0.09), residues: 3580 sheet: -2.62 (0.62), residues: 57 loop : -3.52 (0.15), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A2104 HIS 0.012 0.001 HIS A2151 PHE 0.035 0.001 PHE A2016 TYR 0.057 0.002 TYR B2097 ARG 0.017 0.001 ARG B1932 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 GLN cc_start: 0.9526 (mt0) cc_final: 0.9320 (pm20) REVERT: A 1582 PHE cc_start: 0.9162 (m-80) cc_final: 0.8683 (m-80) REVERT: A 1663 THR cc_start: 0.8673 (p) cc_final: 0.8388 (p) REVERT: A 1683 MET cc_start: 0.8299 (mmm) cc_final: 0.7930 (mmm) REVERT: A 1737 HIS cc_start: 0.8826 (t70) cc_final: 0.7879 (t-90) REVERT: A 1951 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7489 (ptt-90) REVERT: A 1976 LEU cc_start: 0.9536 (mp) cc_final: 0.9067 (mt) REVERT: A 2026 LYS cc_start: 0.9581 (mtmm) cc_final: 0.9318 (mmtm) REVERT: A 2058 MET cc_start: 0.7969 (ptm) cc_final: 0.7081 (ppp) REVERT: A 2093 LEU cc_start: 0.9363 (mt) cc_final: 0.8656 (mt) REVERT: A 2097 TYR cc_start: 0.7837 (m-80) cc_final: 0.7635 (m-80) REVERT: A 2099 THR cc_start: 0.9325 (p) cc_final: 0.8794 (p) REVERT: A 2100 LYS cc_start: 0.9256 (mttt) cc_final: 0.8837 (mmtm) REVERT: A 2151 HIS cc_start: 0.7401 (m-70) cc_final: 0.6761 (m-70) REVERT: A 2155 GLU cc_start: 0.8706 (tp30) cc_final: 0.8454 (tp30) REVERT: A 2225 LEU cc_start: 0.9796 (mt) cc_final: 0.9456 (mt) REVERT: A 2310 LYS cc_start: 0.9213 (mtmt) cc_final: 0.8824 (mppt) REVERT: A 2324 MET cc_start: 0.8905 (mmm) cc_final: 0.8414 (mmm) REVERT: A 2325 MET cc_start: 0.8112 (mmp) cc_final: 0.7618 (mtm) REVERT: A 2339 MET cc_start: 0.8935 (mmt) cc_final: 0.8228 (mmt) REVERT: A 2429 LEU cc_start: 0.9414 (mt) cc_final: 0.8991 (tp) REVERT: A 2437 HIS cc_start: 0.8659 (t70) cc_final: 0.8013 (t70) REVERT: A 2441 LEU cc_start: 0.9563 (mt) cc_final: 0.9333 (mt) REVERT: A 2537 GLU cc_start: 0.9013 (tt0) cc_final: 0.8732 (tt0) REVERT: A 2543 MET cc_start: 0.8975 (mtm) cc_final: 0.8552 (mtm) REVERT: A 2636 MET cc_start: 0.8893 (mmp) cc_final: 0.8692 (mmm) REVERT: B 1575 GLN cc_start: 0.8705 (mt0) cc_final: 0.8337 (mp10) REVERT: B 1582 PHE cc_start: 0.9211 (m-80) cc_final: 0.8874 (m-80) REVERT: B 1651 TYR cc_start: 0.8147 (m-80) cc_final: 0.7684 (m-80) REVERT: B 1804 LEU cc_start: 0.8982 (tp) cc_final: 0.8773 (tp) REVERT: B 1841 ARG cc_start: 0.9097 (mmm-85) cc_final: 0.8679 (tpp80) REVERT: B 1852 VAL cc_start: 0.9647 (t) cc_final: 0.9322 (m) REVERT: B 1961 LYS cc_start: 0.8934 (mtmt) cc_final: 0.8285 (mmtt) REVERT: B 1962 TRP cc_start: 0.8040 (t60) cc_final: 0.7758 (t60) REVERT: B 1996 MET cc_start: 0.8645 (mpp) cc_final: 0.8329 (pmm) REVERT: B 2040 PHE cc_start: 0.7223 (p90) cc_final: 0.6848 (p90) REVERT: B 2052 MET cc_start: 0.8900 (mmm) cc_final: 0.8586 (mmp) REVERT: B 2100 LYS cc_start: 0.9474 (mmtm) cc_final: 0.8948 (mmtt) REVERT: B 2195 LYS cc_start: 0.9457 (mttt) cc_final: 0.9241 (mmmt) REVERT: B 2206 LYS cc_start: 0.9058 (mttt) cc_final: 0.8648 (ptpp) REVERT: B 2339 MET cc_start: 0.9149 (mmt) cc_final: 0.8467 (mmt) REVERT: B 2356 ARG cc_start: 0.8477 (mtt180) cc_final: 0.7664 (mtp85) REVERT: B 2364 THR cc_start: 0.9533 (p) cc_final: 0.8652 (p) REVERT: B 2438 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8543 (mt-10) REVERT: B 2475 ASP cc_start: 0.7829 (t0) cc_final: 0.7557 (t70) REVERT: B 2494 ASP cc_start: 0.7594 (t70) cc_final: 0.7123 (t0) REVERT: B 2529 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7406 (mp0) REVERT: B 2551 MET cc_start: 0.8807 (tpt) cc_final: 0.8433 (tpt) REVERT: B 2594 ASP cc_start: 0.8889 (m-30) cc_final: 0.8293 (m-30) REVERT: B 2596 GLU cc_start: 0.9081 (pt0) cc_final: 0.8822 (pp20) REVERT: B 2597 GLN cc_start: 0.9037 (mp10) cc_final: 0.8353 (mt0) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.4704 time to fit residues: 388.0320 Evaluate side-chains 411 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 5.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 433 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 chunk 7 optimal weight: 0.0970 chunk 387 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 chunk 444 optimal weight: 8.9990 chunk 360 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 266 optimal weight: 30.0000 chunk 467 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 ASN ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2361 HIS ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2559 HIS A2585 ASN ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1789 ASN ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2056 ASN ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2123 ASN ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2227 ASN ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 33737 Z= 0.243 Angle : 0.721 9.654 46276 Z= 0.396 Chirality : 0.043 0.263 5753 Planarity : 0.005 0.097 6264 Dihedral : 7.461 55.252 5588 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.60 % Allowed : 14.63 % Favored : 84.77 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 5364 helix: 0.08 (0.09), residues: 3592 sheet: -2.42 (0.59), residues: 67 loop : -3.57 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A2104 HIS 0.011 0.002 HIS B2153 PHE 0.021 0.002 PHE A2016 TYR 0.041 0.002 TYR B2097 ARG 0.014 0.001 ARG A2074 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 466 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 GLN cc_start: 0.9495 (mt0) cc_final: 0.9287 (pm20) REVERT: A 1582 PHE cc_start: 0.9228 (m-80) cc_final: 0.8723 (m-80) REVERT: A 1663 THR cc_start: 0.8821 (p) cc_final: 0.8576 (p) REVERT: A 1683 MET cc_start: 0.8427 (mmm) cc_final: 0.8036 (mmm) REVERT: A 1737 HIS cc_start: 0.8557 (t70) cc_final: 0.7699 (t-90) REVERT: A 2058 MET cc_start: 0.7965 (ptm) cc_final: 0.7056 (ppp) REVERT: A 2093 LEU cc_start: 0.9530 (mt) cc_final: 0.8781 (mt) REVERT: A 2097 TYR cc_start: 0.7831 (m-80) cc_final: 0.7617 (m-80) REVERT: A 2099 THR cc_start: 0.9191 (p) cc_final: 0.8740 (p) REVERT: A 2100 LYS cc_start: 0.9228 (mttt) cc_final: 0.8840 (mmtm) REVERT: A 2151 HIS cc_start: 0.7509 (m-70) cc_final: 0.5752 (m-70) REVERT: A 2155 GLU cc_start: 0.8851 (tp30) cc_final: 0.8135 (tp30) REVERT: A 2225 LEU cc_start: 0.9783 (mt) cc_final: 0.9536 (mt) REVERT: A 2310 LYS cc_start: 0.9307 (mtmt) cc_final: 0.8946 (mppt) REVERT: A 2324 MET cc_start: 0.9032 (mmm) cc_final: 0.8452 (mmm) REVERT: A 2325 MET cc_start: 0.8331 (mmp) cc_final: 0.7603 (mtm) REVERT: A 2339 MET cc_start: 0.8988 (mmt) cc_final: 0.8356 (mmt) REVERT: A 2429 LEU cc_start: 0.9347 (mt) cc_final: 0.8910 (tp) REVERT: A 2437 HIS cc_start: 0.8739 (t70) cc_final: 0.8303 (t70) REVERT: A 2489 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 2505 PHE cc_start: 0.8285 (t80) cc_final: 0.7764 (t80) REVERT: A 2520 VAL cc_start: 0.9571 (t) cc_final: 0.9189 (t) REVERT: A 2540 MET cc_start: 0.9029 (mmm) cc_final: 0.8753 (mmm) REVERT: A 2543 MET cc_start: 0.8938 (mtm) cc_final: 0.8206 (mtp) REVERT: A 2551 MET cc_start: 0.8710 (tmm) cc_final: 0.8494 (tmm) REVERT: A 2636 MET cc_start: 0.9002 (mmp) cc_final: 0.8714 (mmm) REVERT: B 1575 GLN cc_start: 0.8858 (mt0) cc_final: 0.8456 (mp10) REVERT: B 1582 PHE cc_start: 0.9289 (m-80) cc_final: 0.8867 (m-80) REVERT: B 1769 GLU cc_start: 0.8623 (mp0) cc_final: 0.8327 (mp0) REVERT: B 1776 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8505 (mt-10) REVERT: B 1841 ARG cc_start: 0.8992 (mmm-85) cc_final: 0.8492 (tpt-90) REVERT: B 1932 ARG cc_start: 0.9220 (ttp80) cc_final: 0.8822 (ttp80) REVERT: B 1961 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8527 (mmtt) REVERT: B 1964 TRP cc_start: 0.7798 (t60) cc_final: 0.7484 (t60) REVERT: B 2040 PHE cc_start: 0.7642 (p90) cc_final: 0.7331 (p90) REVERT: B 2052 MET cc_start: 0.9057 (mmm) cc_final: 0.8686 (mmp) REVERT: B 2074 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7519 (ptp-110) REVERT: B 2125 VAL cc_start: 0.9365 (p) cc_final: 0.8747 (p) REVERT: B 2206 LYS cc_start: 0.9044 (mttt) cc_final: 0.8719 (ptpp) REVERT: B 2339 MET cc_start: 0.9194 (mmt) cc_final: 0.8516 (mmt) REVERT: B 2356 ARG cc_start: 0.8539 (mtt180) cc_final: 0.7720 (mtp85) REVERT: B 2390 LEU cc_start: 0.9368 (mt) cc_final: 0.8903 (mp) REVERT: B 2407 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8675 (tpt170) REVERT: B 2438 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 2466 MET cc_start: 0.8978 (mpp) cc_final: 0.8555 (mpp) REVERT: B 2505 PHE cc_start: 0.8791 (t80) cc_final: 0.8507 (t80) REVERT: B 2551 MET cc_start: 0.9024 (tpt) cc_final: 0.8796 (tpt) REVERT: B 2596 GLU cc_start: 0.9147 (pt0) cc_final: 0.8736 (pp20) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.4661 time to fit residues: 357.7271 Evaluate side-chains 392 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 175 optimal weight: 10.0000 chunk 469 optimal weight: 3.9990 chunk 102 optimal weight: 40.0000 chunk 305 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 521 optimal weight: 40.0000 chunk 432 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 GLN ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1830 GLN A1936 HIS ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2019 ASN ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2263 GLN ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33737 Z= 0.265 Angle : 0.729 9.921 46276 Z= 0.402 Chirality : 0.044 0.228 5753 Planarity : 0.005 0.097 6264 Dihedral : 7.397 55.945 5588 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.54 % Allowed : 15.16 % Favored : 84.30 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.50 % 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: -1.33 (0.12), residues: 5364 helix: 0.33 (0.09), residues: 3603 sheet: -2.40 (0.60), residues: 67 loop : -3.56 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A2104 HIS 0.021 0.002 HIS A2129 PHE 0.024 0.002 PHE A2016 TYR 0.036 0.002 TYR B2097 ARG 0.026 0.001 ARG A2074 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1542 GLN cc_start: 0.9492 (mt0) cc_final: 0.9288 (pm20) REVERT: A 1582 PHE cc_start: 0.9221 (m-80) cc_final: 0.8739 (m-80) REVERT: A 1663 THR cc_start: 0.8908 (p) cc_final: 0.8692 (p) REVERT: A 1737 HIS cc_start: 0.8340 (t70) cc_final: 0.7807 (t-90) REVERT: A 1951 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7610 (ptp-170) REVERT: A 2055 ASP cc_start: 0.9150 (p0) cc_final: 0.8871 (p0) REVERT: A 2058 MET cc_start: 0.7943 (ptm) cc_final: 0.7388 (ppp) REVERT: A 2090 MET cc_start: 0.8881 (mmp) cc_final: 0.8124 (mmp) REVERT: A 2093 LEU cc_start: 0.9440 (mt) cc_final: 0.8773 (mt) REVERT: A 2099 THR cc_start: 0.9093 (p) cc_final: 0.8428 (p) REVERT: A 2100 LYS cc_start: 0.9256 (mttt) cc_final: 0.9008 (mmtp) REVERT: A 2144 GLN cc_start: 0.9068 (mp10) cc_final: 0.8849 (mm110) REVERT: A 2151 HIS cc_start: 0.7524 (m-70) cc_final: 0.7238 (m170) REVERT: A 2155 GLU cc_start: 0.8861 (tp30) cc_final: 0.8641 (tp30) REVERT: A 2225 LEU cc_start: 0.9809 (mt) cc_final: 0.9537 (mt) REVERT: A 2310 LYS cc_start: 0.9282 (mtmt) cc_final: 0.9012 (mtmm) REVERT: A 2324 MET cc_start: 0.9009 (mmm) cc_final: 0.8294 (mmm) REVERT: A 2325 MET cc_start: 0.8269 (mmp) cc_final: 0.7646 (mtm) REVERT: A 2339 MET cc_start: 0.8946 (mmt) cc_final: 0.8299 (mmt) REVERT: A 2419 GLU cc_start: 0.9106 (tp30) cc_final: 0.8880 (tp30) REVERT: A 2429 LEU cc_start: 0.9393 (mt) cc_final: 0.9009 (tp) REVERT: A 2437 HIS cc_start: 0.8803 (t70) cc_final: 0.8446 (t70) REVERT: A 2505 PHE cc_start: 0.8297 (t80) cc_final: 0.7768 (t80) REVERT: A 2520 VAL cc_start: 0.9550 (t) cc_final: 0.9336 (t) REVERT: A 2540 MET cc_start: 0.8941 (mmm) cc_final: 0.8713 (mmm) REVERT: A 2543 MET cc_start: 0.8928 (mtm) cc_final: 0.8158 (mtp) REVERT: A 2636 MET cc_start: 0.8981 (mmp) cc_final: 0.8687 (mmm) REVERT: B 1575 GLN cc_start: 0.8868 (mt0) cc_final: 0.8463 (mp10) REVERT: B 1582 PHE cc_start: 0.9294 (m-80) cc_final: 0.8961 (m-80) REVERT: B 1683 MET cc_start: 0.9061 (mtp) cc_final: 0.8821 (mmm) REVERT: B 1741 LYS cc_start: 0.9383 (mmmm) cc_final: 0.8898 (mmmm) REVERT: B 1769 GLU cc_start: 0.8720 (mp0) cc_final: 0.8370 (mp0) REVERT: B 1776 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 1841 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8350 (tpt-90) REVERT: B 1959 ARG cc_start: 0.8792 (pmt170) cc_final: 0.8498 (pmt170) REVERT: B 1961 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8479 (mmtt) REVERT: B 1964 TRP cc_start: 0.7847 (t60) cc_final: 0.7550 (t60) REVERT: B 2040 PHE cc_start: 0.7718 (p90) cc_final: 0.7474 (p90) REVERT: B 2052 MET cc_start: 0.9063 (mmm) cc_final: 0.8692 (mmp) REVERT: B 2074 ARG cc_start: 0.8508 (mtp85) cc_final: 0.7679 (ptp-110) REVERT: B 2115 MET cc_start: 0.8357 (tpt) cc_final: 0.8035 (tpt) REVERT: B 2125 VAL cc_start: 0.9390 (p) cc_final: 0.8892 (p) REVERT: B 2129 HIS cc_start: 0.8612 (t70) cc_final: 0.8209 (t-170) REVERT: B 2206 LYS cc_start: 0.9049 (mttt) cc_final: 0.8774 (ptpp) REVERT: B 2356 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7845 (mtp85) REVERT: B 2405 GLU cc_start: 0.9386 (tt0) cc_final: 0.9130 (tp30) REVERT: B 2407 ARG cc_start: 0.9030 (mtt180) cc_final: 0.8704 (tpt170) REVERT: B 2438 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8615 (mt-10) REVERT: B 2505 PHE cc_start: 0.8804 (t80) cc_final: 0.8526 (t80) REVERT: B 2526 MET cc_start: 0.8254 (tpp) cc_final: 0.8023 (tpp) REVERT: B 2546 GLN cc_start: 0.8109 (mp10) cc_final: 0.7745 (mp10) REVERT: B 2596 GLU cc_start: 0.9122 (pt0) cc_final: 0.8889 (pp20) REVERT: B 2597 GLN cc_start: 0.9025 (mp10) cc_final: 0.8158 (mp10) outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.4681 time to fit residues: 354.9741 Evaluate side-chains 390 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 502 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 297 optimal weight: 20.0000 chunk 380 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 438 optimal weight: 0.3980 chunk 291 optimal weight: 20.0000 chunk 519 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 HIS ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33737 Z= 0.208 Angle : 0.696 11.574 46276 Z= 0.379 Chirality : 0.043 0.278 5753 Planarity : 0.005 0.096 6264 Dihedral : 7.187 55.567 5588 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.45 % Favored : 85.03 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.50 % 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: -1.00 (0.12), residues: 5364 helix: 0.62 (0.09), residues: 3609 sheet: -2.39 (0.59), residues: 67 loop : -3.53 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A2104 HIS 0.011 0.001 HIS B2153 PHE 0.018 0.001 PHE B1582 TYR 0.033 0.002 TYR B2097 ARG 0.012 0.001 ARG A1951 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 470 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1537 LEU cc_start: 0.9278 (mt) cc_final: 0.9066 (mt) REVERT: A 1582 PHE cc_start: 0.9203 (m-80) cc_final: 0.8681 (m-80) REVERT: A 1663 THR cc_start: 0.8886 (p) cc_final: 0.8639 (p) REVERT: A 1683 MET cc_start: 0.8280 (mmm) cc_final: 0.7798 (mmm) REVERT: A 1737 HIS cc_start: 0.8226 (t70) cc_final: 0.7124 (t-90) REVERT: A 1916 TYR cc_start: 0.7782 (p90) cc_final: 0.7556 (p90) REVERT: A 2058 MET cc_start: 0.7989 (ptm) cc_final: 0.7341 (ppp) REVERT: A 2099 THR cc_start: 0.9007 (p) cc_final: 0.8398 (p) REVERT: A 2100 LYS cc_start: 0.9251 (mttt) cc_final: 0.8859 (mmtm) REVERT: A 2140 THR cc_start: 0.8421 (t) cc_final: 0.8032 (t) REVERT: A 2144 GLN cc_start: 0.9076 (mp10) cc_final: 0.8646 (mp10) REVERT: A 2151 HIS cc_start: 0.7565 (m-70) cc_final: 0.6522 (m90) REVERT: A 2155 GLU cc_start: 0.8837 (tp30) cc_final: 0.8184 (tp30) REVERT: A 2225 LEU cc_start: 0.9780 (mt) cc_final: 0.9576 (mt) REVERT: A 2266 MET cc_start: 0.8350 (mmm) cc_final: 0.8108 (pmm) REVERT: A 2310 LYS cc_start: 0.9353 (mtmt) cc_final: 0.9076 (mtmm) REVERT: A 2324 MET cc_start: 0.9052 (mmm) cc_final: 0.8482 (mmm) REVERT: A 2325 MET cc_start: 0.8203 (mmp) cc_final: 0.7604 (mtm) REVERT: A 2339 MET cc_start: 0.8984 (mmt) cc_final: 0.8333 (mmt) REVERT: A 2429 LEU cc_start: 0.9474 (mt) cc_final: 0.9051 (tp) REVERT: A 2437 HIS cc_start: 0.8749 (t70) cc_final: 0.8278 (t70) REVERT: A 2482 LEU cc_start: 0.9008 (mm) cc_final: 0.8661 (mt) REVERT: A 2489 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8305 (mt-10) REVERT: A 2505 PHE cc_start: 0.8301 (t80) cc_final: 0.7746 (t80) REVERT: A 2520 VAL cc_start: 0.9548 (t) cc_final: 0.9293 (t) REVERT: A 2537 GLU cc_start: 0.9012 (tt0) cc_final: 0.8783 (tt0) REVERT: A 2540 MET cc_start: 0.9030 (mmm) cc_final: 0.8708 (mmm) REVERT: A 2543 MET cc_start: 0.8906 (mtm) cc_final: 0.8143 (mtp) REVERT: A 2636 MET cc_start: 0.8953 (mmp) cc_final: 0.8584 (mmm) REVERT: B 1582 PHE cc_start: 0.9246 (m-80) cc_final: 0.9032 (m-80) REVERT: B 1683 MET cc_start: 0.9157 (mtp) cc_final: 0.8910 (mmm) REVERT: B 1704 GLU cc_start: 0.7985 (mp0) cc_final: 0.7783 (mp0) REVERT: B 1769 GLU cc_start: 0.8595 (mp0) cc_final: 0.8172 (mp0) REVERT: B 1841 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8491 (tpt-90) REVERT: B 1852 VAL cc_start: 0.9681 (t) cc_final: 0.9274 (m) REVERT: B 1959 ARG cc_start: 0.8765 (pmt170) cc_final: 0.8498 (pmt170) REVERT: B 1961 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8636 (mmtt) REVERT: B 1962 TRP cc_start: 0.7822 (t60) cc_final: 0.7617 (t60) REVERT: B 1964 TRP cc_start: 0.7802 (t60) cc_final: 0.7506 (t60) REVERT: B 1976 LEU cc_start: 0.9473 (mt) cc_final: 0.9019 (mt) REVERT: B 2017 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7826 (mp0) REVERT: B 2047 ASP cc_start: 0.8758 (t0) cc_final: 0.8535 (t0) REVERT: B 2052 MET cc_start: 0.9063 (mmm) cc_final: 0.8701 (mmp) REVERT: B 2074 ARG cc_start: 0.8396 (mtp85) cc_final: 0.7619 (ptp-110) REVERT: B 2087 MET cc_start: 0.7626 (tpt) cc_final: 0.6984 (tpp) REVERT: B 2125 VAL cc_start: 0.9356 (p) cc_final: 0.8878 (p) REVERT: B 2129 HIS cc_start: 0.8505 (t70) cc_final: 0.8069 (t-170) REVERT: B 2206 LYS cc_start: 0.8986 (mttt) cc_final: 0.8660 (ptpp) REVERT: B 2338 LEU cc_start: 0.9477 (mt) cc_final: 0.9200 (mt) REVERT: B 2339 MET cc_start: 0.9158 (mmt) cc_final: 0.8485 (mmt) REVERT: B 2356 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7716 (mtp85) REVERT: B 2390 LEU cc_start: 0.9399 (mp) cc_final: 0.9037 (mt) REVERT: B 2405 GLU cc_start: 0.9317 (tt0) cc_final: 0.9111 (tp30) REVERT: B 2438 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8580 (mt-10) REVERT: B 2464 MET cc_start: 0.9023 (tpt) cc_final: 0.8631 (tpp) REVERT: B 2505 PHE cc_start: 0.8747 (t80) cc_final: 0.8490 (t80) REVERT: B 2514 ARG cc_start: 0.9248 (tpt170) cc_final: 0.8653 (tpt170) REVERT: B 2529 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 2546 GLN cc_start: 0.8083 (mp10) cc_final: 0.7695 (mp10) REVERT: B 2597 GLN cc_start: 0.9063 (mp10) cc_final: 0.7970 (mp10) REVERT: B 2599 LEU cc_start: 0.9686 (mm) cc_final: 0.9476 (mm) REVERT: B 2636 MET cc_start: 0.8777 (mmm) cc_final: 0.8444 (tpp) outliers start: 0 outliers final: 0 residues processed: 470 average time/residue: 0.4643 time to fit residues: 358.7723 Evaluate side-chains 399 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 321 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 310 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 102 optimal weight: 40.0000 chunk 100 optimal weight: 7.9990 chunk 330 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 256 optimal weight: 0.0170 chunk 48 optimal weight: 0.4980 chunk 408 optimal weight: 0.1980 overall best weight: 1.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 HIS ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2192 ASN ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2019 ASN ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2123 ASN ** B2129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 33737 Z= 0.186 Angle : 0.690 10.677 46276 Z= 0.372 Chirality : 0.043 0.213 5753 Planarity : 0.004 0.097 6264 Dihedral : 7.021 55.046 5588 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.50 % Allowed : 14.21 % Favored : 85.29 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.43 % 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: -0.74 (0.12), residues: 5364 helix: 0.83 (0.09), residues: 3616 sheet: -2.28 (0.58), residues: 67 loop : -3.50 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A2104 HIS 0.009 0.001 HIS B2129 PHE 0.022 0.001 PHE A2557 TYR 0.028 0.002 TYR B1549 ARG 0.010 0.001 ARG A1929 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 4.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1582 PHE cc_start: 0.9188 (m-80) cc_final: 0.8650 (m-80) REVERT: A 1584 MET cc_start: 0.8710 (mpp) cc_final: 0.8284 (mpp) REVERT: A 1663 THR cc_start: 0.8905 (p) cc_final: 0.8648 (p) REVERT: A 1683 MET cc_start: 0.8219 (mmm) cc_final: 0.7736 (mmm) REVERT: A 1737 HIS cc_start: 0.8167 (t70) cc_final: 0.7180 (t-90) REVERT: A 1744 LEU cc_start: 0.9127 (mt) cc_final: 0.8885 (mt) REVERT: A 1955 LEU cc_start: 0.8121 (tp) cc_final: 0.7881 (tp) REVERT: A 2009 PHE cc_start: 0.6982 (m-80) cc_final: 0.6750 (m-80) REVERT: A 2058 MET cc_start: 0.7935 (ptm) cc_final: 0.7286 (ppp) REVERT: A 2099 THR cc_start: 0.9004 (p) cc_final: 0.8741 (p) REVERT: A 2310 LYS cc_start: 0.9322 (mtmt) cc_final: 0.9032 (mtmm) REVERT: A 2325 MET cc_start: 0.8167 (mmp) cc_final: 0.7753 (mtm) REVERT: A 2335 ASP cc_start: 0.8939 (m-30) cc_final: 0.8711 (m-30) REVERT: A 2339 MET cc_start: 0.9018 (mmt) cc_final: 0.8377 (mmt) REVERT: A 2429 LEU cc_start: 0.9458 (mt) cc_final: 0.9025 (tp) REVERT: A 2437 HIS cc_start: 0.8741 (t70) cc_final: 0.8371 (t70) REVERT: A 2482 LEU cc_start: 0.8936 (mm) cc_final: 0.8602 (mt) REVERT: A 2489 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8327 (mt-10) REVERT: A 2505 PHE cc_start: 0.8362 (t80) cc_final: 0.7819 (t80) REVERT: A 2519 MET cc_start: 0.8943 (mtp) cc_final: 0.8734 (mtp) REVERT: A 2533 ARG cc_start: 0.8946 (mtp85) cc_final: 0.8674 (mmm160) REVERT: A 2537 GLU cc_start: 0.8995 (tt0) cc_final: 0.8779 (tt0) REVERT: A 2540 MET cc_start: 0.9057 (mmm) cc_final: 0.8716 (mmm) REVERT: A 2543 MET cc_start: 0.8861 (mtm) cc_final: 0.8176 (mtp) REVERT: A 2624 ILE cc_start: 0.9497 (mt) cc_final: 0.9285 (mt) REVERT: A 2636 MET cc_start: 0.8913 (mmp) cc_final: 0.8586 (mmm) REVERT: B 1582 PHE cc_start: 0.9236 (m-80) cc_final: 0.9027 (m-80) REVERT: B 1683 MET cc_start: 0.9126 (mtp) cc_final: 0.8849 (mmm) REVERT: B 1704 GLU cc_start: 0.8019 (mp0) cc_final: 0.7803 (mp0) REVERT: B 1741 LYS cc_start: 0.9354 (mmmm) cc_final: 0.8867 (mmmm) REVERT: B 1769 GLU cc_start: 0.8505 (mp0) cc_final: 0.8089 (mp0) REVERT: B 1841 ARG cc_start: 0.8906 (mmm-85) cc_final: 0.8483 (tpt-90) REVERT: B 1852 VAL cc_start: 0.9622 (t) cc_final: 0.9350 (m) REVERT: B 1932 ARG cc_start: 0.9368 (tmm160) cc_final: 0.9088 (ttp80) REVERT: B 1955 LEU cc_start: 0.8786 (tp) cc_final: 0.8424 (pp) REVERT: B 1959 ARG cc_start: 0.8754 (pmt170) cc_final: 0.8505 (pmt170) REVERT: B 1961 LYS cc_start: 0.8989 (mtmt) cc_final: 0.8599 (mmtt) REVERT: B 1964 TRP cc_start: 0.7798 (t60) cc_final: 0.7495 (t60) REVERT: B 1976 LEU cc_start: 0.9483 (mt) cc_final: 0.9011 (mt) REVERT: B 2017 GLU cc_start: 0.8658 (mt-10) cc_final: 0.7871 (mp0) REVERT: B 2035 TRP cc_start: 0.7745 (m100) cc_final: 0.7151 (m100) REVERT: B 2040 PHE cc_start: 0.7716 (p90) cc_final: 0.7435 (p90) REVERT: B 2047 ASP cc_start: 0.8765 (t0) cc_final: 0.8511 (t0) REVERT: B 2052 MET cc_start: 0.8990 (mmm) cc_final: 0.8622 (mmp) REVERT: B 2074 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7690 (ptp-110) REVERT: B 2087 MET cc_start: 0.7559 (tpt) cc_final: 0.7146 (tpp) REVERT: B 2125 VAL cc_start: 0.9354 (p) cc_final: 0.8882 (p) REVERT: B 2129 HIS cc_start: 0.8514 (t70) cc_final: 0.8172 (t-170) REVERT: B 2206 LYS cc_start: 0.8996 (mttt) cc_final: 0.8650 (ptpp) REVERT: B 2245 MET cc_start: 0.8352 (tmm) cc_final: 0.8150 (tmm) REVERT: B 2338 LEU cc_start: 0.9492 (mt) cc_final: 0.9171 (mt) REVERT: B 2339 MET cc_start: 0.9182 (mmt) cc_final: 0.8511 (mmt) REVERT: B 2356 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7451 (mtp85) REVERT: B 2390 LEU cc_start: 0.9391 (mp) cc_final: 0.9034 (mt) REVERT: B 2401 MET cc_start: 0.8420 (mmm) cc_final: 0.8176 (mmm) REVERT: B 2438 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8511 (mt-10) REVERT: B 2464 MET cc_start: 0.8844 (tpt) cc_final: 0.8599 (tpp) REVERT: B 2473 LEU cc_start: 0.8646 (pt) cc_final: 0.8103 (mp) REVERT: B 2505 PHE cc_start: 0.8780 (t80) cc_final: 0.8506 (t80) REVERT: B 2529 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6926 (mm-30) REVERT: B 2536 CYS cc_start: 0.7547 (t) cc_final: 0.6856 (t) REVERT: B 2546 GLN cc_start: 0.8085 (mp10) cc_final: 0.7675 (mm-40) REVERT: B 2597 GLN cc_start: 0.8266 (mp10) cc_final: 0.7804 (mp10) REVERT: B 2636 MET cc_start: 0.8711 (mmm) cc_final: 0.8335 (tpp) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.4512 time to fit residues: 345.0990 Evaluate side-chains 389 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 472 optimal weight: 40.0000 chunk 497 optimal weight: 10.0000 chunk 454 optimal weight: 0.7980 chunk 484 optimal weight: 30.0000 chunk 291 optimal weight: 0.9980 chunk 210 optimal weight: 7.9990 chunk 380 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 437 optimal weight: 10.0000 chunk 457 optimal weight: 6.9990 chunk 482 optimal weight: 7.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1748 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1936 HIS ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2123 ASN ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2242 HIS ** B2279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33737 Z= 0.230 Angle : 0.705 14.055 46276 Z= 0.383 Chirality : 0.043 0.251 5753 Planarity : 0.005 0.096 6264 Dihedral : 6.960 54.483 5588 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.52 % Allowed : 14.45 % Favored : 85.03 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 3.00 % Twisted General : 0.45 % 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: -0.67 (0.12), residues: 5364 helix: 0.91 (0.09), residues: 3630 sheet: -2.60 (0.56), residues: 69 loop : -3.55 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP A2104 HIS 0.016 0.002 HIS B2492 PHE 0.019 0.002 PHE B1868 TYR 0.036 0.002 TYR A2102 ARG 0.010 0.001 ARG A2217 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 4.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1582 PHE cc_start: 0.9208 (m-80) cc_final: 0.8694 (m-80) REVERT: A 1584 MET cc_start: 0.8744 (mpp) cc_final: 0.8312 (mpp) REVERT: A 1663 THR cc_start: 0.8928 (p) cc_final: 0.8715 (p) REVERT: A 1683 MET cc_start: 0.8339 (mmm) cc_final: 0.7804 (mmm) REVERT: A 1710 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 1737 HIS cc_start: 0.8114 (t70) cc_final: 0.7440 (t-170) REVERT: A 1744 LEU cc_start: 0.9083 (mt) cc_final: 0.8881 (mt) REVERT: A 2009 PHE cc_start: 0.7322 (m-80) cc_final: 0.7089 (m-80) REVERT: A 2058 MET cc_start: 0.8010 (ptm) cc_final: 0.7356 (ppp) REVERT: A 2090 MET cc_start: 0.8590 (mmp) cc_final: 0.7766 (mmp) REVERT: A 2094 TRP cc_start: 0.7987 (m100) cc_final: 0.7189 (m100) REVERT: A 2099 THR cc_start: 0.9111 (p) cc_final: 0.8237 (p) REVERT: A 2138 PHE cc_start: 0.8973 (m-80) cc_final: 0.8638 (m-80) REVERT: A 2225 LEU cc_start: 0.9739 (mt) cc_final: 0.9419 (mt) REVERT: A 2310 LYS cc_start: 0.9287 (mtmt) cc_final: 0.9042 (mtmm) REVERT: A 2324 MET cc_start: 0.8952 (mmm) cc_final: 0.8099 (mmp) REVERT: A 2325 MET cc_start: 0.8226 (mmp) cc_final: 0.7705 (mtm) REVERT: A 2339 MET cc_start: 0.8972 (mmt) cc_final: 0.8352 (mmt) REVERT: A 2429 LEU cc_start: 0.9368 (mt) cc_final: 0.8898 (tp) REVERT: A 2437 HIS cc_start: 0.8722 (t70) cc_final: 0.8297 (t70) REVERT: A 2505 PHE cc_start: 0.8444 (t80) cc_final: 0.7643 (t80) REVERT: A 2519 MET cc_start: 0.9017 (mtp) cc_final: 0.8786 (mtp) REVERT: A 2533 ARG cc_start: 0.8986 (mtp85) cc_final: 0.8691 (mmm160) REVERT: A 2540 MET cc_start: 0.9060 (mmm) cc_final: 0.8766 (mmm) REVERT: A 2543 MET cc_start: 0.8879 (mtm) cc_final: 0.8159 (mtp) REVERT: A 2624 ILE cc_start: 0.9514 (mt) cc_final: 0.9260 (mt) REVERT: A 2636 MET cc_start: 0.8943 (mmp) cc_final: 0.8630 (mmm) REVERT: B 1582 PHE cc_start: 0.9245 (m-80) cc_final: 0.9041 (m-80) REVERT: B 1683 MET cc_start: 0.9130 (mtp) cc_final: 0.8831 (mmm) REVERT: B 1741 LYS cc_start: 0.9361 (mmmm) cc_final: 0.8831 (mmmm) REVERT: B 1769 GLU cc_start: 0.8553 (mp0) cc_final: 0.8152 (mp0) REVERT: B 1776 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8735 (mt-10) REVERT: B 1841 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8507 (tpt-90) REVERT: B 1895 ARG cc_start: 0.9276 (mpp80) cc_final: 0.9057 (mpp80) REVERT: B 1932 ARG cc_start: 0.9508 (tmm160) cc_final: 0.9122 (tmm160) REVERT: B 1959 ARG cc_start: 0.8795 (pmt170) cc_final: 0.8494 (pmt170) REVERT: B 1961 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8600 (mmtt) REVERT: B 1964 TRP cc_start: 0.7890 (t60) cc_final: 0.7511 (t60) REVERT: B 1970 HIS cc_start: 0.9100 (m-70) cc_final: 0.8789 (m170) REVERT: B 2035 TRP cc_start: 0.7854 (m100) cc_final: 0.7206 (m100) REVERT: B 2040 PHE cc_start: 0.7890 (p90) cc_final: 0.7602 (p90) REVERT: B 2052 MET cc_start: 0.9012 (mmm) cc_final: 0.8683 (mmp) REVERT: B 2087 MET cc_start: 0.7701 (tpt) cc_final: 0.7024 (tpp) REVERT: B 2097 TYR cc_start: 0.7002 (m-80) cc_final: 0.6748 (m-80) REVERT: B 2129 HIS cc_start: 0.8524 (t70) cc_final: 0.7960 (t-170) REVERT: B 2178 MET cc_start: 0.9422 (mpp) cc_final: 0.9002 (mpp) REVERT: B 2206 LYS cc_start: 0.9002 (mttt) cc_final: 0.8685 (ptpp) REVERT: B 2339 MET cc_start: 0.9185 (mmt) cc_final: 0.8500 (mmt) REVERT: B 2356 ARG cc_start: 0.8343 (mtt180) cc_final: 0.7733 (mtp85) REVERT: B 2464 MET cc_start: 0.8880 (tpt) cc_final: 0.8656 (tpp) REVERT: B 2505 PHE cc_start: 0.8764 (t80) cc_final: 0.8498 (t80) REVERT: B 2529 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6995 (mm-30) REVERT: B 2546 GLN cc_start: 0.8189 (mp10) cc_final: 0.7910 (mm-40) REVERT: B 2557 PHE cc_start: 0.8759 (t80) cc_final: 0.8553 (t80) REVERT: B 2644 MET cc_start: 0.8003 (tpt) cc_final: 0.7244 (mmm) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.5009 time to fit residues: 378.3506 Evaluate side-chains 386 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 317 optimal weight: 8.9990 chunk 511 optimal weight: 0.4980 chunk 312 optimal weight: 30.0000 chunk 242 optimal weight: 4.9990 chunk 355 optimal weight: 6.9990 chunk 536 optimal weight: 3.9990 chunk 494 optimal weight: 30.0000 chunk 427 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 330 optimal weight: 20.0000 chunk 262 optimal weight: 0.8980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1748 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS ** B2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 33737 Z= 0.177 Angle : 0.684 12.148 46276 Z= 0.366 Chirality : 0.043 0.267 5753 Planarity : 0.004 0.096 6264 Dihedral : 6.783 54.060 5588 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.81 % Favored : 85.66 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.52 % Twisted Proline : 2.58 % Twisted General : 0.39 % 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: -0.40 (0.12), residues: 5364 helix: 1.14 (0.09), residues: 3622 sheet: -2.50 (0.56), residues: 69 loop : -3.49 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A2104 HIS 0.012 0.001 HIS B2492 PHE 0.022 0.001 PHE A2557 TYR 0.032 0.002 TYR A2102 ARG 0.014 0.001 ARG A1929 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10728 Ramachandran restraints generated. 5364 Oldfield, 0 Emsley, 5364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 4.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1582 PHE cc_start: 0.9178 (m-80) cc_final: 0.8622 (m-80) REVERT: A 1584 MET cc_start: 0.8750 (mpp) cc_final: 0.8318 (mpp) REVERT: A 1586 ASP cc_start: 0.9016 (m-30) cc_final: 0.8797 (m-30) REVERT: A 1663 THR cc_start: 0.8970 (p) cc_final: 0.8769 (p) REVERT: A 1683 MET cc_start: 0.8181 (mmm) cc_final: 0.7693 (mmm) REVERT: A 1737 HIS cc_start: 0.8156 (t70) cc_final: 0.7350 (t-90) REVERT: A 1744 LEU cc_start: 0.9041 (mt) cc_final: 0.8835 (mt) REVERT: A 1910 LEU cc_start: 0.9361 (tp) cc_final: 0.9100 (tt) REVERT: A 1932 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8561 (mtm-85) REVERT: A 1961 LYS cc_start: 0.8293 (mptt) cc_final: 0.7870 (mmtm) REVERT: A 2058 MET cc_start: 0.7914 (ptm) cc_final: 0.7219 (ppp) REVERT: A 2070 LEU cc_start: 0.9294 (mm) cc_final: 0.9007 (mm) REVERT: A 2074 ARG cc_start: 0.8419 (tmt-80) cc_final: 0.7367 (ptm-80) REVERT: A 2090 MET cc_start: 0.8449 (mmp) cc_final: 0.7731 (mmp) REVERT: A 2094 TRP cc_start: 0.8040 (m100) cc_final: 0.7226 (m100) REVERT: A 2099 THR cc_start: 0.9050 (p) cc_final: 0.8799 (p) REVERT: A 2140 THR cc_start: 0.8203 (t) cc_final: 0.7976 (t) REVERT: A 2223 LEU cc_start: 0.9406 (mt) cc_final: 0.9176 (tp) REVERT: A 2225 LEU cc_start: 0.9663 (mt) cc_final: 0.9461 (mt) REVERT: A 2266 MET cc_start: 0.8121 (mmm) cc_final: 0.7848 (tpt) REVERT: A 2324 MET cc_start: 0.8962 (mmm) cc_final: 0.8394 (mmm) REVERT: A 2325 MET cc_start: 0.8623 (mmp) cc_final: 0.7920 (mtm) REVERT: A 2339 MET cc_start: 0.8995 (mmt) cc_final: 0.8284 (mmt) REVERT: A 2429 LEU cc_start: 0.9425 (mt) cc_final: 0.8910 (tp) REVERT: A 2437 HIS cc_start: 0.8689 (t70) cc_final: 0.8388 (t70) REVERT: A 2469 TYR cc_start: 0.9285 (t80) cc_final: 0.8885 (t80) REVERT: A 2533 ARG cc_start: 0.8966 (mtp85) cc_final: 0.8657 (mmm160) REVERT: A 2537 GLU cc_start: 0.8915 (tt0) cc_final: 0.8681 (tt0) REVERT: A 2624 ILE cc_start: 0.9481 (mt) cc_final: 0.9270 (mt) REVERT: A 2636 MET cc_start: 0.8898 (mmp) cc_final: 0.8538 (mmm) REVERT: B 1582 PHE cc_start: 0.9160 (m-80) cc_final: 0.8932 (m-80) REVERT: B 1704 GLU cc_start: 0.7987 (mp0) cc_final: 0.7655 (mp0) REVERT: B 1724 ARG cc_start: 0.8966 (ptm160) cc_final: 0.7882 (mmm160) REVERT: B 1741 LYS cc_start: 0.9350 (mmmm) cc_final: 0.8826 (mmmm) REVERT: B 1769 GLU cc_start: 0.8362 (mp0) cc_final: 0.8091 (mp0) REVERT: B 1841 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8442 (tpt-90) REVERT: B 1932 ARG cc_start: 0.9464 (tmm160) cc_final: 0.9045 (tmm160) REVERT: B 1959 ARG cc_start: 0.8757 (pmt170) cc_final: 0.8482 (pmt170) REVERT: B 1961 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8592 (mmtt) REVERT: B 1964 TRP cc_start: 0.7785 (t60) cc_final: 0.7332 (t60) REVERT: B 1976 LEU cc_start: 0.9377 (mt) cc_final: 0.8971 (mt) REVERT: B 2017 GLU cc_start: 0.8690 (mt-10) cc_final: 0.7907 (mp0) REVERT: B 2040 PHE cc_start: 0.7746 (p90) cc_final: 0.7453 (p90) REVERT: B 2047 ASP cc_start: 0.8696 (t0) cc_final: 0.8484 (t0) REVERT: B 2052 MET cc_start: 0.8940 (mmm) cc_final: 0.8623 (mmp) REVERT: B 2087 MET cc_start: 0.7582 (tpt) cc_final: 0.6980 (tpp) REVERT: B 2129 HIS cc_start: 0.8451 (t70) cc_final: 0.7910 (t70) REVERT: B 2139 LEU cc_start: 0.8842 (mt) cc_final: 0.8640 (mt) REVERT: B 2178 MET cc_start: 0.9415 (mpp) cc_final: 0.8909 (mpp) REVERT: B 2206 LYS cc_start: 0.9002 (mttt) cc_final: 0.8656 (ptpp) REVERT: B 2339 MET cc_start: 0.9186 (mmt) cc_final: 0.8650 (mmt) REVERT: B 2342 ASN cc_start: 0.9563 (m110) cc_final: 0.9323 (m110) REVERT: B 2356 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7265 (mtp85) REVERT: B 2401 MET cc_start: 0.8230 (mmm) cc_final: 0.8007 (mmm) REVERT: B 2505 PHE cc_start: 0.8836 (t80) cc_final: 0.8549 (t80) REVERT: B 2529 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6756 (mm-30) REVERT: B 2546 GLN cc_start: 0.8175 (mp10) cc_final: 0.7765 (mm-40) REVERT: B 2593 LEU cc_start: 0.9063 (mm) cc_final: 0.7801 (pp) REVERT: B 2596 GLU cc_start: 0.7519 (pp20) cc_final: 0.7135 (pp20) REVERT: B 2636 MET cc_start: 0.8586 (tpp) cc_final: 0.7739 (tpt) REVERT: B 2644 MET cc_start: 0.8054 (tpt) cc_final: 0.7850 (mmm) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.4499 time to fit residues: 344.9275 Evaluate side-chains 389 residues out of total 4814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 539 random chunks: chunk 339 optimal weight: 40.0000 chunk 455 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 chunk 394 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 428 optimal weight: 9.9990 chunk 179 optimal weight: 0.9990 chunk 439 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 78 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1748 GLN ** A1760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1789 ASN ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2283 HIS ** A2480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2015 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2019 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2077 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2123 ASN ** B2129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2432 HIS B2480 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.075948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.055952 restraints weight = 185512.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.057767 restraints weight = 115401.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.059034 restraints weight = 81376.204| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33737 Z= 0.175 Angle : 0.679 10.746 46276 Z= 0.363 Chirality : 0.042 0.288 5753 Planarity : 0.004 0.094 6264 Dihedral : 6.648 53.639 5588 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.40 % Favored : 86.07 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.50 % Twisted Proline : 2.58 % Twisted General : 0.43 % 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: -0.27 (0.13), residues: 5364 helix: 1.26 (0.09), residues: 3629 sheet: -2.52 (0.56), residues: 69 loop : -3.52 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A2104 HIS 0.011 0.001 HIS A2492 PHE 0.022 0.001 PHE A2016 TYR 0.029 0.002 TYR A2102 ARG 0.011 0.001 ARG B1951 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7564.86 seconds wall clock time: 137 minutes 30.34 seconds (8250.34 seconds total)