Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 11 22:40:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pw5_20499/07_2023/6pw5_20499_updated.pdb" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 190 5.16 5 C 15986 2.51 5 N 4036 2.21 5 O 4500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 366": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 484": "NH1" <-> "NH2" Residue "A ARG 501": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A ARG 771": "NH1" <-> "NH2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 250": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B ARG 366": "NH1" <-> "NH2" Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 749": "NH1" <-> "NH2" Residue "B ARG 759": "NH1" <-> "NH2" Residue "B ARG 761": "NH1" <-> "NH2" Residue "B ARG 771": "NH1" <-> "NH2" Residue "B ARG 772": "NH1" <-> "NH2" Residue "B ARG 794": "NH1" <-> "NH2" Residue "B PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 851": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 366": "NH1" <-> "NH2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ARG 472": "NH1" <-> "NH2" Residue "C PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 484": "NH1" <-> "NH2" Residue "C ARG 501": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C ARG 759": "NH1" <-> "NH2" Residue "C ARG 771": "NH1" <-> "NH2" Residue "C ARG 794": "NH1" <-> "NH2" Residue "C PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 828": "NH1" <-> "NH2" Residue "C ARG 836": "NH1" <-> "NH2" Residue "C ARG 846": "NH1" <-> "NH2" Residue "C ARG 851": "NH1" <-> "NH2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 366": "NH1" <-> "NH2" Residue "D PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "D ARG 501": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D ARG 644": "NH1" <-> "NH2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 749": "NH1" <-> "NH2" Residue "D ARG 759": "NH1" <-> "NH2" Residue "D ARG 761": "NH1" <-> "NH2" Residue "D ARG 771": "NH1" <-> "NH2" Residue "D ARG 772": "NH1" <-> "NH2" Residue "D ARG 794": "NH1" <-> "NH2" Residue "D PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 809": "NH1" <-> "NH2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ARG 851": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 24740 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5858 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 26, 'TRANS': 707} Chain breaks: 3 Chain: "B" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6197 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 753} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 5858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5858 Classifications: {'peptide': 734} Link IDs: {'PTRANS': 26, 'TRANS': 707} Chain breaks: 3 Chain: "D" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6197 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 753} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 164 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 164 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'PCW': 1, 'PIK': 1, 'PIO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PCW:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 11.98, per 1000 atoms: 0.48 Number of scatterers: 24740 At special positions: 0 Unit cell: (159.6, 160.55, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 190 16.00 P 28 15.00 O 4500 8.00 N 4036 7.00 C 15986 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 668 " - pdb=" SG CYS A 678 " distance=2.03 Simple disulfide: pdb=" SG CYS B 668 " - pdb=" SG CYS B 678 " distance=2.03 Simple disulfide: pdb=" SG CYS C 668 " - pdb=" SG CYS C 678 " distance=2.04 Simple disulfide: pdb=" SG CYS D 668 " - pdb=" SG CYS D 678 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.97 Conformation dependent library (CDL) restraints added in 3.2 seconds 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 0 sheets defined 58.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 93 through 96 No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.690A pdb=" N VAL A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 removed outlier: 3.927A pdb=" N ALA A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 119 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.536A pdb=" N ALA A 134 " --> pdb=" O SER A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.776A pdb=" N TYR A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.708A pdb=" N GLU A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 219 removed outlier: 4.092A pdb=" N LEU A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 4.100A pdb=" N SER A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE A 241 " --> pdb=" O VAL A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.544A pdb=" N GLY A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 removed outlier: 3.510A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.830A pdb=" N ALA A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 407 through 410 No H-bonds generated for 'chain 'A' and resid 407 through 410' Processing helix chain 'A' and resid 424 through 432 removed outlier: 3.558A pdb=" N THR A 429 " --> pdb=" O GLN A 425 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS A 431 " --> pdb=" O ILE A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 461 through 473 Proline residue: A 466 - end of helix removed outlier: 3.560A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 removed outlier: 3.530A pdb=" N PHE A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 498 through 521 removed outlier: 4.049A pdb=" N PHE A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 539 through 555 Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.795A pdb=" N THR A 574 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 579 " --> pdb=" O MET A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 619 removed outlier: 3.551A pdb=" N VAL A 601 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 606 " --> pdb=" O ASN A 603 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 608 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 610 " --> pdb=" O ALA A 607 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET A 612 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 613 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 615 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 618 " --> pdb=" O PHE A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 639 removed outlier: 4.015A pdb=" N MET A 633 " --> pdb=" O PRO A 629 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 664 removed outlier: 3.684A pdb=" N VAL A 651 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 750 removed outlier: 3.562A pdb=" N LEU A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 741 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 removed outlier: 4.741A pdb=" N ARG A 759 " --> pdb=" O MET A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 766 No H-bonds generated for 'chain 'A' and resid 763 through 766' Processing helix chain 'A' and resid 780 through 796 removed outlier: 3.508A pdb=" N LEU A 784 " --> pdb=" O ASN A 780 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 855 removed outlier: 3.685A pdb=" N ASN A 843 " --> pdb=" O ASP A 839 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL A 847 " --> pdb=" O ASN A 843 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 868 removed outlier: 4.093A pdb=" N HIS A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 867 " --> pdb=" O HIS A 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.610A pdb=" N GLN B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 65 through 73 removed outlier: 3.655A pdb=" N LEU B 71 " --> pdb=" O LYS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 99 through 107 Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 140 through 152 removed outlier: 4.296A pdb=" N TYR B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.684A pdb=" N ALA B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 4.099A pdb=" N VAL B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.925A pdb=" N LEU B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 4.326A pdb=" N SER B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 257 removed outlier: 3.902A pdb=" N GLU B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 347 removed outlier: 3.736A pdb=" N SER B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 369 through 385 removed outlier: 3.564A pdb=" N ALA B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN B 374 " --> pdb=" O ASP B 370 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 383 " --> pdb=" O GLU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 3.858A pdb=" N ALA B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 416 through 419 No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 424 through 432 removed outlier: 3.753A pdb=" N PHE B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 431 " --> pdb=" O ILE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 removed outlier: 3.781A pdb=" N LYS B 442 " --> pdb=" O ASP B 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.574A pdb=" N LEU B 454 " --> pdb=" O GLY B 450 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 474 removed outlier: 3.978A pdb=" N SER B 473 " --> pdb=" O VAL B 469 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 483 removed outlier: 3.596A pdb=" N ASP B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 521 removed outlier: 3.577A pdb=" N TRP B 502 " --> pdb=" O PRO B 498 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 511 " --> pdb=" O CYS B 507 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 512 " --> pdb=" O ALA B 508 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 521 " --> pdb=" O SER B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.699A pdb=" N ALA B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 548 " --> pdb=" O CYS B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 565 No H-bonds generated for 'chain 'B' and resid 563 through 565' Processing helix chain 'B' and resid 569 through 591 removed outlier: 3.609A pdb=" N VAL B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 576 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 591 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 614 removed outlier: 3.737A pdb=" N LEU B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 601 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 607 " --> pdb=" O ASN B 603 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 613 " --> pdb=" O ALA B 609 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 622 removed outlier: 4.022A pdb=" N VAL B 620 " --> pdb=" O MET B 617 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B 622 " --> pdb=" O SER B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 640 removed outlier: 3.515A pdb=" N MET B 634 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N MET B 637 " --> pdb=" O MET B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 663 removed outlier: 4.834A pdb=" N LEU B 647 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL B 651 " --> pdb=" O LEU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 752 removed outlier: 4.399A pdb=" N GLY B 720 " --> pdb=" O LYS B 716 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 723 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 734 " --> pdb=" O VAL B 730 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 748 " --> pdb=" O ALA B 744 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 766 Processing helix chain 'B' and resid 777 through 784 removed outlier: 4.713A pdb=" N LEU B 781 " --> pdb=" O PRO B 777 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B 782 " --> pdb=" O PRO B 778 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS B 783 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 790 No H-bonds generated for 'chain 'B' and resid 787 through 790' Processing helix chain 'B' and resid 792 through 796 removed outlier: 4.335A pdb=" N LEU B 796 " --> pdb=" O LEU B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 841 removed outlier: 3.535A pdb=" N VAL B 832 " --> pdb=" O ARG B 828 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 840 " --> pdb=" O ARG B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 856 removed outlier: 3.870A pdb=" N ALA B 848 " --> pdb=" O SER B 844 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 852 " --> pdb=" O ALA B 848 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 871 removed outlier: 3.701A pdb=" N GLN B 868 " --> pdb=" O GLU B 864 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LYS B 869 " --> pdb=" O MET B 865 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 870 " --> pdb=" O LEU B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 65 through 74 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'C' and resid 100 through 107 removed outlier: 3.665A pdb=" N VAL C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 removed outlier: 3.929A pdb=" N ALA C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET C 119 " --> pdb=" O GLU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.537A pdb=" N ALA C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.780A pdb=" N TYR C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 177 Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.709A pdb=" N GLU C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 219 removed outlier: 4.092A pdb=" N LEU C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 241 removed outlier: 4.101A pdb=" N SER C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.544A pdb=" N GLY C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 removed outlier: 3.510A pdb=" N LEU C 362 " --> pdb=" O CYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.829A pdb=" N ALA C 373 " --> pdb=" O ASP C 369 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN C 374 " --> pdb=" O ASP C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 395 No H-bonds generated for 'chain 'C' and resid 392 through 395' Processing helix chain 'C' and resid 407 through 410 No H-bonds generated for 'chain 'C' and resid 407 through 410' Processing helix chain 'C' and resid 424 through 427 No H-bonds generated for 'chain 'C' and resid 424 through 427' Processing helix chain 'C' and resid 429 through 432 No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 461 through 473 Proline residue: C 466 - end of helix removed outlier: 3.570A pdb=" N ALA C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 482 removed outlier: 3.531A pdb=" N PHE C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 498 through 521 removed outlier: 4.033A pdb=" N PHE C 512 " --> pdb=" O ALA C 508 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 539 through 555 Processing helix chain 'C' and resid 560 through 564 Processing helix chain 'C' and resid 569 through 587 removed outlier: 3.794A pdb=" N THR C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR C 579 " --> pdb=" O MET C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 619 removed outlier: 3.552A pdb=" N VAL C 601 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 603 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 606 " --> pdb=" O ASN C 603 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 608 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 609 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 610 " --> pdb=" O ALA C 607 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET C 612 " --> pdb=" O ALA C 609 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 613 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE C 615 " --> pdb=" O MET C 612 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 618 " --> pdb=" O PHE C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 639 removed outlier: 3.512A pdb=" N GLN C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET C 633 " --> pdb=" O PRO C 629 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 664 removed outlier: 3.686A pdb=" N VAL C 651 " --> pdb=" O LEU C 647 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 750 removed outlier: 3.564A pdb=" N LEU C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 741 " --> pdb=" O ASN C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 766 removed outlier: 4.706A pdb=" N ARG C 759 " --> pdb=" O MET C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 796 removed outlier: 3.514A pdb=" N LEU C 784 " --> pdb=" O ASN C 780 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG C 794 " --> pdb=" O GLY C 790 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 796 " --> pdb=" O GLY C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 868 removed outlier: 3.686A pdb=" N ASN C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL C 847 " --> pdb=" O ASN C 843 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE C 850 " --> pdb=" O ARG C 846 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 852 " --> pdb=" O ALA C 848 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 857 " --> pdb=" O LYS C 853 " (cutoff:3.500A) Proline residue: C 859 - end of helix removed outlier: 4.090A pdb=" N HIS C 863 " --> pdb=" O PRO C 859 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 864 " --> pdb=" O ASN C 860 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS C 867 " --> pdb=" O HIS C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 26 removed outlier: 3.610A pdb=" N GLN D 25 " --> pdb=" O ASP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 50 No H-bonds generated for 'chain 'D' and resid 47 through 50' Processing helix chain 'D' and resid 65 through 73 removed outlier: 3.655A pdb=" N LEU D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 114 through 120 Processing helix chain 'D' and resid 140 through 152 removed outlier: 4.296A pdb=" N TYR D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 151 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 removed outlier: 3.684A pdb=" N ALA D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 192 removed outlier: 4.100A pdb=" N VAL D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 219 removed outlier: 3.926A pdb=" N LEU D 211 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 214 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 4.326A pdb=" N SER D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 257 removed outlier: 3.903A pdb=" N GLU D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 347 removed outlier: 3.736A pdb=" N SER D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 369 through 385 removed outlier: 3.564A pdb=" N ALA D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN D 374 " --> pdb=" O ASP D 370 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 395 removed outlier: 3.858A pdb=" N ALA D 394 " --> pdb=" O GLN D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 416 through 419 No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 424 through 432 removed outlier: 3.752A pdb=" N PHE D 428 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 429 " --> pdb=" O GLN D 425 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS D 431 " --> pdb=" O ILE D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 442 removed outlier: 3.783A pdb=" N LYS D 442 " --> pdb=" O ASP D 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 447 through 462 removed outlier: 3.574A pdb=" N LEU D 454 " --> pdb=" O GLY D 450 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL D 455 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 474 removed outlier: 3.984A pdb=" N SER D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 474 " --> pdb=" O VAL D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 483 removed outlier: 3.611A pdb=" N ASP D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 521 removed outlier: 3.576A pdb=" N TRP D 502 " --> pdb=" O PRO D 498 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 511 " --> pdb=" O CYS D 507 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE D 512 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 521 " --> pdb=" O SER D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 535 through 556 removed outlier: 3.699A pdb=" N ALA D 541 " --> pdb=" O ASN D 537 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU D 548 " --> pdb=" O CYS D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 569 through 591 removed outlier: 3.609A pdb=" N VAL D 573 " --> pdb=" O ASN D 569 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 584 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG D 591 " --> pdb=" O ILE D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 614 removed outlier: 3.736A pdb=" N LEU D 600 " --> pdb=" O LEU D 596 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 601 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 607 " --> pdb=" O ASN D 603 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 613 " --> pdb=" O ALA D 609 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP D 614 " --> pdb=" O ALA D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 622 removed outlier: 4.041A pdb=" N VAL D 620 " --> pdb=" O MET D 617 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 622 " --> pdb=" O SER D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 640 removed outlier: 3.533A pdb=" N MET D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET D 637 " --> pdb=" O MET D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 663 removed outlier: 4.839A pdb=" N LEU D 647 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 648 " --> pdb=" O ARG D 644 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL D 651 " --> pdb=" O LEU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 716 through 752 removed outlier: 4.395A pdb=" N GLY D 720 " --> pdb=" O LYS D 716 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL D 721 " --> pdb=" O ARG D 717 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE D 723 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 734 " --> pdb=" O VAL D 730 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 738 " --> pdb=" O LEU D 734 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 742 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP D 745 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 749 " --> pdb=" O ASP D 745 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 766 Processing helix chain 'D' and resid 777 through 784 removed outlier: 4.714A pdb=" N LEU D 781 " --> pdb=" O PRO D 777 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU D 782 " --> pdb=" O PRO D 778 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS D 783 " --> pdb=" O PHE D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 790 No H-bonds generated for 'chain 'D' and resid 787 through 790' Processing helix chain 'D' and resid 793 through 796 No H-bonds generated for 'chain 'D' and resid 793 through 796' Processing helix chain 'D' and resid 825 through 856 removed outlier: 3.534A pdb=" N VAL D 832 " --> pdb=" O ARG D 828 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP D 840 " --> pdb=" O ARG D 836 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER D 844 " --> pdb=" O ASP D 840 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 848 " --> pdb=" O SER D 844 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU D 852 " --> pdb=" O ALA D 848 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 856 " --> pdb=" O GLU D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 871 removed outlier: 3.701A pdb=" N GLN D 868 " --> pdb=" O GLU D 864 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS D 869 " --> pdb=" O MET D 865 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY D 870 " --> pdb=" O LEU D 866 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.94 Time building geometry restraints manager: 9.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3898 1.30 - 1.43: 6803 1.43 - 1.57: 14229 1.57 - 1.70: 42 1.70 - 1.83: 308 Bond restraints: 25280 Sorted by residual: bond pdb=" C11 PCW B1002 " pdb=" O3 PCW B1002 " ideal model delta sigma weight residual 1.326 1.398 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C11 PCW D1002 " pdb=" O3 PCW D1002 " ideal model delta sigma weight residual 1.326 1.397 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" N PCW C1002 " pdb=" C5 PCW C1002 " ideal model delta sigma weight residual 1.510 1.439 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N PCW B1002 " pdb=" C5 PCW B1002 " ideal model delta sigma weight residual 1.510 1.440 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N PCW D1002 " pdb=" C5 PCW D1002 " ideal model delta sigma weight residual 1.510 1.441 0.069 2.00e-02 2.50e+03 1.21e+01 ... (remaining 25275 not shown) Histogram of bond angle deviations from ideal: 96.47 - 104.07: 378 104.07 - 111.67: 10957 111.67 - 119.27: 10168 119.27 - 126.88: 12354 126.88 - 134.48: 413 Bond angle restraints: 34270 Sorted by residual: angle pdb=" N VAL A 380 " pdb=" CA VAL A 380 " pdb=" C VAL A 380 " ideal model delta sigma weight residual 113.42 105.89 7.53 1.17e+00 7.31e-01 4.15e+01 angle pdb=" N VAL C 380 " pdb=" CA VAL C 380 " pdb=" C VAL C 380 " ideal model delta sigma weight residual 113.42 105.89 7.53 1.17e+00 7.31e-01 4.15e+01 angle pdb=" C GLY A 75 " pdb=" N GLN A 76 " pdb=" CA GLN A 76 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C GLY C 75 " pdb=" N GLN C 76 " pdb=" CA GLN C 76 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" N SER B 683 " pdb=" CA SER B 683 " pdb=" C SER B 683 " ideal model delta sigma weight residual 112.12 119.81 -7.69 1.34e+00 5.57e-01 3.29e+01 ... (remaining 34265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 14624 32.91 - 65.82: 334 65.82 - 98.73: 29 98.73 - 131.63: 5 131.63 - 164.54: 4 Dihedral angle restraints: 14996 sinusoidal: 6110 harmonic: 8886 Sorted by residual: dihedral pdb=" CA PRO B 272 " pdb=" C PRO B 272 " pdb=" N THR B 273 " pdb=" CA THR B 273 " ideal model delta harmonic sigma weight residual -180.00 -110.03 -69.97 0 5.00e+00 4.00e-02 1.96e+02 dihedral pdb=" CA PRO D 272 " pdb=" C PRO D 272 " pdb=" N THR D 273 " pdb=" CA THR D 273 " ideal model delta harmonic sigma weight residual -180.00 -112.98 -67.02 0 5.00e+00 4.00e-02 1.80e+02 dihedral pdb=" CA ARG B 231 " pdb=" C ARG B 231 " pdb=" N SER B 232 " pdb=" CA SER B 232 " ideal model delta harmonic sigma weight residual -180.00 -130.03 -49.97 0 5.00e+00 4.00e-02 9.99e+01 ... (remaining 14993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 3426 0.095 - 0.191: 413 0.191 - 0.286: 43 0.286 - 0.381: 5 0.381 - 0.476: 1 Chirality restraints: 3888 Sorted by residual: chirality pdb=" CB VAL C 618 " pdb=" CA VAL C 618 " pdb=" CG1 VAL C 618 " pdb=" CG2 VAL C 618 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CB VAL A 618 " pdb=" CA VAL A 618 " pdb=" CG1 VAL A 618 " pdb=" CG2 VAL A 618 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" C2 PCW A1002 " pdb=" C1 PCW A1002 " pdb=" C3 PCW A1002 " pdb=" O2 PCW A1002 " both_signs ideal model delta sigma weight residual False -2.32 -1.98 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 3885 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 231 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C ARG D 231 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG D 231 " 0.029 2.00e-02 2.50e+03 pdb=" N SER D 232 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 231 " 0.023 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ARG B 231 " -0.078 2.00e-02 2.50e+03 pdb=" O ARG B 231 " 0.029 2.00e-02 2.50e+03 pdb=" N SER B 232 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 543 " 0.028 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP C 543 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 543 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP C 543 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 543 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 543 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 543 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 543 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 543 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 543 " 0.002 2.00e-02 2.50e+03 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8191 2.84 - 3.36: 22465 3.36 - 3.87: 38833 3.87 - 4.39: 47855 4.39 - 4.90: 79038 Nonbonded interactions: 196382 Sorted by model distance: nonbonded pdb=" NH1 ARG C 501 " pdb=" O TYR C 769 " model vdw 2.327 2.520 nonbonded pdb=" NH1 ARG A 501 " pdb=" O TYR A 769 " model vdw 2.328 2.520 nonbonded pdb=" O ILE C 78 " pdb=" OG SER C 89 " model vdw 2.346 2.440 nonbonded pdb=" NE1 TRP D 568 " pdb=" OE2 GLU D 622 " model vdw 2.351 2.520 nonbonded pdb=" NE1 TRP B 568 " pdb=" OE2 GLU B 622 " model vdw 2.351 2.520 ... (remaining 196377 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' and (resid 17 through 325 or resid 327 through 811 or (resid 812 and \ (name N or name CA or name C or name O or name CB )) or resid 813 through 872 or \ resid 1001 or (resid 1002 and (name N or name C1 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C2 or name C20 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 or name C \ 40 or name C41 or name C42 or name C43 or name C5 or name C6 or name C7 or name \ C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ O3P or name O4P or name P )) or resid 1003)) selection = (chain 'B' and (resid 17 through 33 or resid 53 through 246 or resid 268 or resi \ d 276 or resid 327 through 872 or resid 1001 through 1003)) selection = (chain 'C' and (resid 17 through 325 or resid 327 through 811 or (resid 812 and \ (name N or name CA or name C or name O or name CB )) or resid 813 through 872 or \ resid 1001 or (resid 1002 and (name N or name C1 or name C11 or name C12 or nam \ e C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or \ name C2 or name C20 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C4 or name C \ 40 or name C41 or name C42 or name C43 or name C5 or name C6 or name C7 or name \ C8 or name O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name \ O3P or name O4P or name P )) or resid 1003)) selection = (chain 'D' and (resid 17 through 33 or resid 53 through 246 or resid 268 or resi \ d 276 or resid 327 through 872 or resid 1001 through 1003)) } 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 individual isotropic 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.240 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 56.390 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.013 0.095 25280 Z= 0.818 Angle : 1.386 18.180 34270 Z= 0.690 Chirality : 0.067 0.476 3888 Planarity : 0.009 0.082 4220 Dihedral : 14.175 164.543 9236 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.77 % Allowed : 11.62 % Favored : 87.62 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.95 (0.09), residues: 3004 helix: -4.65 (0.05), residues: 1920 sheet: None (None), residues: 0 loop : -4.17 (0.14), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 548 time to evaluate : 2.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 11 residues processed: 578 average time/residue: 0.4019 time to fit residues: 349.1287 Evaluate side-chains 363 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 352 time to evaluate : 2.926 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3532 time to fit residues: 10.3360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 143 optimal weight: 40.0000 chunk 176 optimal weight: 0.9980 chunk 274 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 HIS A 97 ASN A 177 GLN A 179 HIS A 364 GLN ** A 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 GLN B 120 HIS B 152 GLN B 177 GLN B 179 HIS B 479 GLN B 506 GLN B 665 GLN B 676 ASN B 737 ASN B 843 ASN B 860 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS C 97 ASN C 177 GLN C 179 HIS C 364 GLN ** C 553 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN D 120 HIS D 152 GLN D 177 GLN D 179 HIS D 479 GLN D 506 GLN D 665 GLN D 676 ASN D 737 ASN D 860 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 25280 Z= 0.168 Angle : 0.647 10.176 34270 Z= 0.333 Chirality : 0.039 0.187 3888 Planarity : 0.006 0.068 4220 Dihedral : 12.232 147.606 3616 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.62 % Favored : 89.98 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.68 (0.12), residues: 3004 helix: -2.70 (0.09), residues: 1928 sheet: None (None), residues: 0 loop : -3.66 (0.16), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 482 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 27 residues processed: 533 average time/residue: 0.3641 time to fit residues: 307.9398 Evaluate side-chains 377 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 350 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2380 time to fit residues: 15.8797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 152 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 chunk 274 optimal weight: 20.0000 chunk 296 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 220 optimal weight: 1.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN B 152 GLN B 359 GLN B 553 GLN B 569 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN D 86 HIS D 359 GLN D 553 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 25280 Z= 0.282 Angle : 0.675 9.339 34270 Z= 0.343 Chirality : 0.041 0.166 3888 Planarity : 0.005 0.068 4220 Dihedral : 11.906 145.292 3616 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.89 % Favored : 89.71 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -3.45 (0.14), residues: 3004 helix: -1.62 (0.11), residues: 1954 sheet: None (None), residues: 0 loop : -3.47 (0.17), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 371 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 50 residues processed: 430 average time/residue: 0.3405 time to fit residues: 237.8395 Evaluate side-chains 375 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 325 time to evaluate : 2.676 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.2269 time to fit residues: 25.1135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 271 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 603 ASN B 152 GLN B 359 GLN B 553 GLN B 632 GLN B 665 GLN B 863 HIS ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 GLN D 553 GLN D 569 ASN D 665 GLN D 863 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 25280 Z= 0.226 Angle : 0.628 15.183 34270 Z= 0.315 Chirality : 0.040 0.163 3888 Planarity : 0.005 0.071 4220 Dihedral : 11.432 141.494 3616 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.75 % Favored : 89.85 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.15), residues: 3004 helix: -1.00 (0.12), residues: 1962 sheet: None (None), residues: 0 loop : -3.39 (0.17), residues: 1042 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 375 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 416 average time/residue: 0.3520 time to fit residues: 236.9412 Evaluate side-chains 358 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 331 time to evaluate : 2.814 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2447 time to fit residues: 15.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 243 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 249 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN B 152 GLN B 737 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN C 553 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 25280 Z= 0.270 Angle : 0.656 12.804 34270 Z= 0.329 Chirality : 0.041 0.159 3888 Planarity : 0.005 0.073 4220 Dihedral : 11.341 142.454 3616 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.95 % Favored : 89.58 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.41 (0.15), residues: 3004 helix: -0.71 (0.12), residues: 1976 sheet: None (None), residues: 0 loop : -3.33 (0.17), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 359 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 30 residues processed: 396 average time/residue: 0.3392 time to fit residues: 218.8944 Evaluate side-chains 359 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 329 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2379 time to fit residues: 17.0375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 98 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 135 optimal weight: 40.0000 chunk 24 optimal weight: 0.7980 chunk 96 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN B 86 HIS B 359 GLN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 25280 Z= 0.473 Angle : 0.767 11.117 34270 Z= 0.382 Chirality : 0.046 0.179 3888 Planarity : 0.005 0.074 4220 Dihedral : 11.960 155.096 3616 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.62 % Favored : 88.85 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.17 % 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: -2.45 (0.15), residues: 3004 helix: -0.73 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -3.31 (0.17), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 338 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 16 residues processed: 368 average time/residue: 0.3496 time to fit residues: 208.3782 Evaluate side-chains 331 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 315 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2510 time to fit residues: 11.0371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 281 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 213 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 245 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 134 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN A 843 ASN B 359 GLN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 GLN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 843 ASN C 855 ASN D 359 GLN D 632 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 25280 Z= 0.160 Angle : 0.587 9.548 34270 Z= 0.299 Chirality : 0.038 0.153 3888 Planarity : 0.004 0.076 4220 Dihedral : 10.785 135.491 3616 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.02 % Favored : 90.65 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.73 (0.16), residues: 3004 helix: -0.11 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -3.18 (0.17), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 375 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 6 residues processed: 388 average time/residue: 0.3368 time to fit residues: 214.3198 Evaluate side-chains 335 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 329 time to evaluate : 2.636 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3564 time to fit residues: 6.9863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 180 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 87 optimal weight: 0.0670 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 ASN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 737 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 25280 Z= 0.257 Angle : 0.641 13.944 34270 Z= 0.322 Chirality : 0.040 0.161 3888 Planarity : 0.005 0.077 4220 Dihedral : 10.788 138.954 3616 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.55 % Favored : 90.05 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.16), residues: 3004 helix: -0.06 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -3.16 (0.18), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 335 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 360 average time/residue: 0.3230 time to fit residues: 192.0040 Evaluate side-chains 346 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 323 time to evaluate : 2.788 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2397 time to fit residues: 14.2280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 264 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 254 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 212 optimal weight: 0.0870 chunk 83 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 256 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25280 Z= 0.217 Angle : 0.622 14.479 34270 Z= 0.312 Chirality : 0.040 0.158 3888 Planarity : 0.005 0.077 4220 Dihedral : 10.573 136.697 3616 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.15 % Favored : 90.45 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.44 (0.16), residues: 3004 helix: 0.12 (0.12), residues: 1960 sheet: None (None), residues: 0 loop : -3.10 (0.18), residues: 1044 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 335 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 348 average time/residue: 0.3486 time to fit residues: 198.5181 Evaluate side-chains 333 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 318 time to evaluate : 2.850 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2441 time to fit residues: 10.6023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 178 optimal weight: 8.9990 chunk 286 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 199 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 276 optimal weight: 10.0000 chunk 239 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 185 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN B 251 GLN ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 ASN D 76 GLN D 251 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25280 Z= 0.159 Angle : 0.585 14.625 34270 Z= 0.295 Chirality : 0.038 0.152 3888 Planarity : 0.004 0.078 4220 Dihedral : 10.104 135.631 3616 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.59 % Favored : 91.05 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.05 (0.16), residues: 3004 helix: 0.46 (0.13), residues: 1942 sheet: None (None), residues: 0 loop : -2.98 (0.18), residues: 1062 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6008 Ramachandran restraints generated. 3004 Oldfield, 0 Emsley, 3004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 356 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 361 average time/residue: 0.3411 time to fit residues: 204.2879 Evaluate side-chains 334 residues out of total 2616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 327 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2611 time to fit residues: 7.0052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 190 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.150039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.106819 restraints weight = 30661.323| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.87 r_work: 0.2887 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 25280 Z= 0.298 Angle : 0.665 14.645 34270 Z= 0.333 Chirality : 0.042 0.275 3888 Planarity : 0.005 0.077 4220 Dihedral : 10.419 145.627 3616 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.39 % Favored : 90.25 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.21 (0.16), residues: 3004 helix: 0.33 (0.12), residues: 1944 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 1060 =============================================================================== Job complete usr+sys time: 5321.30 seconds wall clock time: 97 minutes 21.69 seconds (5841.69 seconds total)