Starting phenix.real_space_refine (version: dev) on Fri Feb 24 23:07:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/02_2023/6ira_9714_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/02_2023/6ira_9714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/02_2023/6ira_9714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/02_2023/6ira_9714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/02_2023/6ira_9714_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/02_2023/6ira_9714_neut.pdb" } resolution = 4.5 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= 0.018 sd= 1.311 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 23932 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 5907 Chain: "A" Number of atoms: 6175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 6290 Chain: "B" Number of atoms: 5791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 5907 Chain: "C" Number of atoms: 6175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 6290 Time building chain proxies: 23.86, per 1000 atoms: 1.00 Number of scatterers: 23932 At special positions: 0 Unit cell: (111.1, 146.45, 187.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 4392 8.00 N 4040 7.00 C 15358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " 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=0, symmetry=0 Time building additional restraints: 9.14 Conformation dependent library (CDL) restraints added in 6.8 seconds 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 36 sheets defined 43.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'D' and resid 45 through 60 Proline residue: D 57 - end of helix removed outlier: 4.296A pdb=" N ALA D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.513A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 116 " --> pdb=" O MET D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.597A pdb=" N TYR D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.877A pdb=" N SER D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.765A pdb=" N SER D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.812A pdb=" N ARG D 291 " --> pdb=" O SER D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 515 through 522 removed outlier: 3.840A pdb=" N VAL D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 581 Processing helix chain 'D' and resid 602 through 613 removed outlier: 3.811A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 611 " --> pdb=" O LEU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 653 removed outlier: 3.693A pdb=" N VAL D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TRP D 634 " --> pdb=" O MET D 630 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR D 645 " --> pdb=" O PHE D 641 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 649 " --> pdb=" O TYR D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 673 through 676 Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 698 through 706 Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.722A pdb=" N ALA D 716 " --> pdb=" O GLY D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.654A pdb=" N GLY D 740 " --> pdb=" O ASN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 785 removed outlier: 3.512A pdb=" N ILE D 775 " --> pdb=" O TRP D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 799 through 803 Processing helix chain 'D' and resid 819 through 836 removed outlier: 3.556A pdb=" N ILE D 836 " --> pdb=" O LEU D 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.772A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.466A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.927A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.608A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.612A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.693A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.536A pdb=" N ALA A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.552A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.801A pdb=" N ALA A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 4.344A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 580 Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.558A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 657 removed outlier: 3.850A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.717A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.906A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.683A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.558A pdb=" N LYS A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.772A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 60 Proline residue: B 57 - end of helix removed outlier: 4.411A pdb=" N ALA B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.539A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.613A pdb=" N TYR B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.872A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.800A pdb=" N SER B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.770A pdb=" N ARG B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.501A pdb=" N ASP B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.618A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 579 Processing helix chain 'B' and resid 602 through 613 removed outlier: 3.916A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 653 removed outlier: 3.612A pdb=" N MET B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 645 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 649 " --> pdb=" O TYR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.751A pdb=" N ALA B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.613A pdb=" N GLY B 740 " --> pdb=" O ASN B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 785 removed outlier: 3.510A pdb=" N ILE B 775 " --> pdb=" O TRP B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 799 through 803 Processing helix chain 'B' and resid 819 through 837 removed outlier: 3.632A pdb=" N ILE B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP B 837 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.772A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 104 through 113 removed outlier: 4.466A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.928A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.609A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.613A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.693A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.545A pdb=" N ALA C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.552A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.801A pdb=" N ALA C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 4.344A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 580 Processing helix chain 'C' and resid 604 through 615 removed outlier: 3.555A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 657 removed outlier: 3.850A pdb=" N LEU C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.716A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.906A pdb=" N TYR C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.683A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.558A pdb=" N LYS C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 810 through 844 removed outlier: 3.773A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 68 through 73 removed outlier: 3.973A pdb=" N GLY D 101 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU D 98 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE D 127 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N PHE D 100 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 199 through 205 removed outlier: 8.542A pdb=" N PHE D 170 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL D 226 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 230 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 229 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 277 through 280 removed outlier: 6.202A pdb=" N VAL D 365 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS D 374 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'D' and resid 405 through 410 Processing sheet with id=AA6, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'D' and resid 523 through 524 Processing sheet with id=AA8, first strand: chain 'D' and resid 682 through 683 removed outlier: 4.298A pdb=" N GLY D 683 " --> pdb=" O ALA D 727 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 729 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 534 " --> pdb=" O TYR D 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 60 through 62 removed outlier: 5.995A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 120 removed outlier: 6.406A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.610A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.241A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.674A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.680A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.680A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AB8, first strand: chain 'A' and resid 487 through 490 removed outlier: 4.560A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.742A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 3.902A pdb=" N GLY B 97 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 37 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 101 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 127 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE B 100 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 199 through 205 removed outlier: 8.652A pdb=" N PHE B 170 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 230 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 277 through 280 removed outlier: 6.116A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AC5, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.508A pdb=" N ASP B 476 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AC7, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AC8, first strand: chain 'B' and resid 728 through 731 Processing sheet with id=AC9, first strand: chain 'C' and resid 60 through 62 removed outlier: 5.996A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.406A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.610A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.242A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.674A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 478 removed outlier: 5.681A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 473 through 478 removed outlier: 5.681A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AD8, first strand: chain 'C' and resid 487 through 490 removed outlier: 4.560A pdb=" N LYS C 495 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 728 through 732 removed outlier: 3.742A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2959 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: 8.53 Time building geometry restraints manager: 9.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4757 1.33 - 1.45: 6454 1.45 - 1.58: 12983 1.58 - 1.70: 0 1.70 - 1.83: 248 Bond restraints: 24442 Sorted by residual: bond pdb=" C LYS B 628 " pdb=" N ILE B 629 " ideal model delta sigma weight residual 1.333 1.445 -0.112 1.31e-02 5.83e+03 7.28e+01 bond pdb=" C GLY B 753 " pdb=" N TYR B 754 " ideal model delta sigma weight residual 1.331 1.444 -0.114 1.45e-02 4.76e+03 6.16e+01 bond pdb=" C GLY D 753 " pdb=" N TYR D 754 " ideal model delta sigma weight residual 1.331 1.444 -0.114 1.45e-02 4.76e+03 6.15e+01 bond pdb=" C SER D 519 " pdb=" N GLU D 520 " ideal model delta sigma weight residual 1.335 1.233 0.102 1.31e-02 5.83e+03 6.02e+01 bond pdb=" N THR A 230 " pdb=" CA THR A 230 " ideal model delta sigma weight residual 1.459 1.375 0.084 1.20e-02 6.94e+03 4.96e+01 ... (remaining 24437 not shown) Histogram of bond angle deviations from ideal: 94.97 - 104.17: 372 104.17 - 113.38: 14096 113.38 - 122.58: 15157 122.58 - 131.79: 3445 131.79 - 140.99: 62 Bond angle restraints: 33132 Sorted by residual: angle pdb=" CA VAL C 246 " pdb=" C VAL C 246 " pdb=" N TRP C 247 " ideal model delta sigma weight residual 116.16 140.99 -24.83 9.60e-01 1.09e+00 6.69e+02 angle pdb=" CA VAL A 246 " pdb=" C VAL A 246 " pdb=" N TRP A 247 " ideal model delta sigma weight residual 116.16 140.97 -24.81 9.60e-01 1.09e+00 6.68e+02 angle pdb=" O VAL C 246 " pdb=" C VAL C 246 " pdb=" N TRP C 247 " ideal model delta sigma weight residual 122.67 97.69 24.98 1.04e+00 9.25e-01 5.77e+02 angle pdb=" O VAL A 246 " pdb=" C VAL A 246 " pdb=" N TRP A 247 " ideal model delta sigma weight residual 122.67 97.70 24.97 1.04e+00 9.25e-01 5.76e+02 angle pdb=" N PRO B 64 " pdb=" CA PRO B 64 " pdb=" C PRO B 64 " ideal model delta sigma weight residual 113.53 94.97 18.56 1.39e+00 5.18e-01 1.78e+02 ... (remaining 33127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 14030 16.27 - 32.53: 465 32.53 - 48.80: 11 48.80 - 65.06: 4 65.06 - 81.33: 4 Dihedral angle restraints: 14514 sinusoidal: 5578 harmonic: 8936 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual -86.00 -167.33 81.33 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -166.79 80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual -86.00 -164.15 78.15 1 1.00e+01 1.00e-02 7.63e+01 ... (remaining 14511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3321 0.105 - 0.209: 400 0.209 - 0.314: 49 0.314 - 0.418: 18 0.418 - 0.523: 2 Chirality restraints: 3790 Sorted by residual: chirality pdb=" CA PHE B 636 " pdb=" N PHE B 636 " pdb=" C PHE B 636 " pdb=" CB PHE B 636 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" CA PHE D 636 " pdb=" N PHE D 636 " pdb=" C PHE D 636 " pdb=" CB PHE D 636 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA GLU C 210 " pdb=" N GLU C 210 " pdb=" C GLU C 210 " pdb=" CB GLU C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 3787 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 628 " 0.043 2.00e-02 2.50e+03 9.47e-02 8.96e+01 pdb=" C LYS B 628 " -0.163 2.00e-02 2.50e+03 pdb=" O LYS B 628 " 0.069 2.00e-02 2.50e+03 pdb=" N ILE B 629 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 247 " -0.038 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C TRP C 247 " 0.121 2.00e-02 2.50e+03 pdb=" O TRP C 247 " -0.043 2.00e-02 2.50e+03 pdb=" N LEU C 248 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 247 " 0.038 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C TRP A 247 " -0.121 2.00e-02 2.50e+03 pdb=" O TRP A 247 " 0.043 2.00e-02 2.50e+03 pdb=" N LEU A 248 " 0.040 2.00e-02 2.50e+03 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 20 2.11 - 2.81: 6704 2.81 - 3.51: 32266 3.51 - 4.20: 54312 4.20 - 4.90: 87899 Nonbonded interactions: 181201 Sorted by model distance: nonbonded pdb=" O VAL D 535 " pdb=" N ILE D 750 " model vdw 1.413 2.520 nonbonded pdb=" O VAL B 535 " pdb=" N ILE B 750 " model vdw 1.423 2.520 nonbonded pdb=" OH TYR C 232 " pdb=" CB ALA C 262 " model vdw 1.439 3.460 nonbonded pdb=" O ALA C 228 " pdb=" CB TYR C 232 " model vdw 1.448 2.752 nonbonded pdb=" CG1 VAL B 522 " pdb=" O LEU B 765 " model vdw 1.621 3.460 ... (remaining 181196 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 25 through 775 or resid 777 through 844)) selection = (chain 'C' and (resid 25 through 775 or resid 777 through 844)) } ncs_group { reference = (chain 'B' and (resid 34 through 700 or resid 702 through 841)) selection = (chain 'D' and (resid 34 through 700 or resid 702 through 841)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 15358 2.51 5 N 4040 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 5.270 Check model and map are aligned: 0.360 Process input model: 76.450 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 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 : 0.009 0.114 24442 Z= 0.573 Angle : 1.419 24.980 33132 Z= 0.909 Chirality : 0.075 0.523 3790 Planarity : 0.008 0.115 4182 Dihedral : 8.452 53.892 8704 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.02 % Favored : 89.12 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.53 (0.13), residues: 3028 helix: -2.37 (0.11), residues: 1212 sheet: -0.84 (0.29), residues: 300 loop : -2.64 (0.15), residues: 1516 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1033 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 1036 average time/residue: 0.3915 time to fit residues: 603.1152 Evaluate side-chains 625 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 624 time to evaluate : 2.815 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2033 time to fit residues: 4.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 128 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 239 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 277 optimal weight: 0.6980 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 96 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN D 674 HIS A 38 HIS A 61 ASN A 86 GLN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 171 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN A 440 ASN A 449 HIS A 520 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 85 HIS B 96 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 367 ASN B 444 ASN ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 61 ASN C 73 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 161 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 375 ASN C 405 GLN C 440 ASN C 449 HIS C 521 ASN ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.094 24442 Z= 0.312 Angle : 0.859 15.906 33132 Z= 0.466 Chirality : 0.053 0.386 3790 Planarity : 0.005 0.059 4182 Dihedral : 7.958 38.932 3280 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.76 % Favored : 90.97 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.86 % 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: -2.76 (0.14), residues: 3028 helix: -1.37 (0.13), residues: 1238 sheet: -0.83 (0.29), residues: 294 loop : -2.46 (0.16), residues: 1496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 759 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 760 average time/residue: 0.3666 time to fit residues: 425.6863 Evaluate side-chains 554 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 2.817 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 231 optimal weight: 0.0010 chunk 189 optimal weight: 0.0570 chunk 76 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 247 optimal weight: 0.1980 chunk 276 optimal weight: 2.9990 chunk 94 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 overall best weight: 0.8306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN D 96 HIS D 153 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS D 515 ASN D 697 ASN ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 341 ASN C 520 ASN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 24442 Z= 0.211 Angle : 0.763 12.714 33132 Z= 0.403 Chirality : 0.050 0.318 3790 Planarity : 0.005 0.070 4182 Dihedral : 7.075 34.605 3280 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.80 % Favored : 91.93 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.15), residues: 3028 helix: -0.75 (0.14), residues: 1246 sheet: -0.62 (0.31), residues: 292 loop : -2.12 (0.16), residues: 1490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 727 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 728 average time/residue: 0.3682 time to fit residues: 412.6438 Evaluate side-chains 573 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 573 time to evaluate : 2.952 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 7.9990 chunk 209 optimal weight: 9.9990 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 295 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 79 optimal weight: 0.0030 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN D 153 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 ASN A 73 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 650 ASN ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 24442 Z= 0.222 Angle : 0.727 11.995 33132 Z= 0.389 Chirality : 0.049 0.296 3790 Planarity : 0.005 0.069 4182 Dihedral : 6.779 34.629 3280 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.40 % Favored : 91.34 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -1.84 (0.15), residues: 3028 helix: -0.50 (0.14), residues: 1256 sheet: -0.69 (0.31), residues: 292 loop : -1.98 (0.16), residues: 1480 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 683 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 683 average time/residue: 0.3599 time to fit residues: 386.5831 Evaluate side-chains 555 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 555 time to evaluate : 3.045 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 HIS D 153 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS B 432 ASN B 697 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.6674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 24442 Z= 0.281 Angle : 0.750 10.535 33132 Z= 0.406 Chirality : 0.049 0.336 3790 Planarity : 0.005 0.052 4182 Dihedral : 6.653 33.264 3280 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.52 % Favored : 90.21 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -1.78 (0.15), residues: 3028 helix: -0.40 (0.14), residues: 1228 sheet: -0.80 (0.31), residues: 282 loop : -1.93 (0.16), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 667 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 668 average time/residue: 0.3563 time to fit residues: 372.1450 Evaluate side-chains 532 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 2.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 6.9990 chunk 266 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 296 optimal weight: 3.9990 chunk 245 optimal weight: 8.9990 chunk 137 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 155 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN A 499 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 24442 Z= 0.264 Angle : 0.754 10.929 33132 Z= 0.402 Chirality : 0.050 0.344 3790 Planarity : 0.005 0.070 4182 Dihedral : 6.634 33.176 3280 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.36 % Favored : 90.38 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -1.75 (0.15), residues: 3028 helix: -0.36 (0.14), residues: 1232 sheet: -0.84 (0.31), residues: 268 loop : -1.92 (0.16), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 669 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.3601 time to fit residues: 379.9750 Evaluate side-chains 541 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.1980 chunk 33 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 167 optimal weight: 0.9980 chunk 249 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN D 494 ASN D 515 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 687 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 705 HIS C 709 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 24442 Z= 0.198 Angle : 0.720 11.048 33132 Z= 0.379 Chirality : 0.050 0.347 3790 Planarity : 0.004 0.062 4182 Dihedral : 6.328 32.653 3280 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.64 % Favored : 92.10 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -1.55 (0.15), residues: 3028 helix: -0.17 (0.14), residues: 1230 sheet: -0.92 (0.31), residues: 278 loop : -1.79 (0.16), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.3554 time to fit residues: 371.8008 Evaluate side-chains 535 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 2.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 30.0000 chunk 117 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 187 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 268 optimal weight: 0.8980 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN D 201 GLN D 264 ASN D 515 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** C 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 24442 Z= 0.272 Angle : 0.764 11.633 33132 Z= 0.406 Chirality : 0.050 0.325 3790 Planarity : 0.005 0.057 4182 Dihedral : 6.355 32.297 3280 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.76 % Favored : 89.98 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % 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: -1.60 (0.15), residues: 3028 helix: -0.21 (0.14), residues: 1232 sheet: -0.89 (0.31), residues: 268 loop : -1.82 (0.16), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 633 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 634 average time/residue: 0.3469 time to fit residues: 346.6613 Evaluate side-chains 510 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 510 time to evaluate : 2.178 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 274 optimal weight: 30.0000 chunk 165 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 152 GLN D 264 ASN D 323 GLN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.8374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 24442 Z= 0.240 Angle : 0.745 11.375 33132 Z= 0.395 Chirality : 0.050 0.364 3790 Planarity : 0.005 0.095 4182 Dihedral : 6.310 31.998 3280 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.63 % Favored : 91.10 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 3028 helix: -0.20 (0.14), residues: 1242 sheet: -0.90 (0.30), residues: 292 loop : -1.86 (0.16), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 642 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 642 average time/residue: 0.3478 time to fit residues: 353.5874 Evaluate side-chains 519 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.887 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 137 optimal weight: 0.0980 chunk 202 optimal weight: 8.9990 chunk 304 optimal weight: 7.9990 chunk 280 optimal weight: 0.9980 chunk 242 optimal weight: 20.0000 chunk 25 optimal weight: 0.1980 chunk 187 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS C 177 GLN C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 650 ASN ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.8617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 24442 Z= 0.199 Angle : 0.728 10.106 33132 Z= 0.381 Chirality : 0.050 0.379 3790 Planarity : 0.004 0.064 4182 Dihedral : 6.102 31.906 3280 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.40 % Favored : 91.34 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.48 (0.15), residues: 3028 helix: -0.08 (0.15), residues: 1244 sheet: -0.83 (0.30), residues: 304 loop : -1.81 (0.16), residues: 1480 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 648 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 648 average time/residue: 0.3653 time to fit residues: 375.9445 Evaluate side-chains 529 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 2.852 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 249 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 213 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 ASN ** D 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.111331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084698 restraints weight = 172573.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088822 restraints weight = 93799.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091797 restraints weight = 61561.712| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.8855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 24442 Z= 0.218 Angle : 0.735 9.780 33132 Z= 0.387 Chirality : 0.050 0.369 3790 Planarity : 0.004 0.061 4182 Dihedral : 6.062 31.621 3280 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.76 % Favored : 90.97 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.42 (0.15), residues: 3028 helix: 0.01 (0.14), residues: 1232 sheet: -0.85 (0.30), residues: 294 loop : -1.79 (0.16), residues: 1502 =============================================================================== Job complete usr+sys time: 6618.77 seconds wall clock time: 120 minutes 10.91 seconds (7210.91 seconds total)