Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:32:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/02_2023/5vot_8721_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/02_2023/5vot_8721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/02_2023/5vot_8721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/02_2023/5vot_8721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/02_2023/5vot_8721_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/02_2023/5vot_8721_neut.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16463 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3049 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 30} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 3046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3046 Classifications: {'peptide': 408} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 31} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 395} Chain breaks: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3028 Classifications: {'peptide': 409} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 38} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 92 Chain: "E" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1007 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 4 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 177 Chain: "F" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1149 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 152 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1007 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 2, 'TRANS': 166} Chain breaks: 4 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 282 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 177 Chain: "H" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1149 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 172} Chain breaks: 3 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 152 Chain: "B" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3028 Classifications: {'peptide': 409} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 38} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 396} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 92 Time building chain proxies: 9.46, per 1000 atoms: 0.57 Number of scatterers: 16463 At special positions: 0 Unit cell: (125.56, 115.24, 147.92, 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 95 16.00 O 3040 8.00 N 2666 7.00 C 10662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " 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: 7.02 Conformation dependent library (CDL) restraints added in 2.6 seconds 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4228 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 24 sheets defined 59.6% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.521A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 571 removed outlier: 3.504A pdb=" N PHE A 571 " --> pdb=" O THR A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 568 through 571' Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 625 removed outlier: 4.517A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 removed outlier: 3.600A pdb=" N LEU A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 685 through 695 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.663A pdb=" N LYS A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 825 removed outlier: 4.170A pdb=" N ALA A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 513 through 517 Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.523A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 571 removed outlier: 3.501A pdb=" N PHE C 571 " --> pdb=" O THR C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 568 through 571' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 625 removed outlier: 4.493A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 641 removed outlier: 3.600A pdb=" N LEU C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 675 Processing helix chain 'C' and resid 685 through 695 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.689A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 825 removed outlier: 5.476A pdb=" N ILE C 798 " --> pdb=" O GLY C 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 512 through 518 removed outlier: 4.273A pdb=" N PHE D 515 " --> pdb=" O PRO D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 545 Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 597 through 621 removed outlier: 3.787A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 removed outlier: 3.593A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.923A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 768 removed outlier: 3.585A pdb=" N LYS D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 824 removed outlier: 3.725A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY D 801 " --> pdb=" O TYR D 797 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 30 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 105 through 127 removed outlier: 3.661A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 160 removed outlier: 3.554A pdb=" N SER E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 212 removed outlier: 3.901A pdb=" N TYR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 30 removed outlier: 3.518A pdb=" N THR F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 103 Processing helix chain 'F' and resid 105 through 127 removed outlier: 4.568A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.861A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 213 removed outlier: 3.645A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 213 " --> pdb=" O ARG F 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 30 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 105 through 127 removed outlier: 3.664A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 160 removed outlier: 3.533A pdb=" N SER G 137 " --> pdb=" O ASN G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 211 removed outlier: 3.899A pdb=" N TYR G 181 " --> pdb=" O GLY G 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 30 removed outlier: 3.523A pdb=" N THR H 30 " --> pdb=" O ILE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 105 through 127 removed outlier: 4.570A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.870A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 213 removed outlier: 3.636A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG H 213 " --> pdb=" O ARG H 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 512 through 518 removed outlier: 4.271A pdb=" N PHE B 515 " --> pdb=" O PRO B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 545 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 597 through 621 removed outlier: 3.787A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 641 removed outlier: 3.592A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.922A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 removed outlier: 3.581A pdb=" N LYS B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 824 removed outlier: 3.724A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY B 801 " --> pdb=" O TYR B 797 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B 810 " --> pdb=" O ALA B 806 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.655A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.294A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 439 through 444 Processing sheet with id=AA7, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AA9, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.653A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.297A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 440 through 444 Processing sheet with id=AB3, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.884A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.234A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 33 through 36 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AB9, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AC1, first strand: chain 'H' and resid 33 through 36 Processing sheet with id=AC2, first strand: chain 'B' and resid 440 through 444 Processing sheet with id=AC3, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AC4, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.879A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.247A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3165 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: 5.34 Time building geometry restraints manager: 7.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5185 1.34 - 1.46: 4239 1.46 - 1.58: 7217 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 16791 Sorted by residual: bond pdb=" C GLY A 588 " pdb=" N CYS A 589 " ideal model delta sigma weight residual 1.330 1.535 -0.206 1.37e-02 5.33e+03 2.26e+02 bond pdb=" N GLN A 587 " pdb=" CA GLN A 587 " ideal model delta sigma weight residual 1.457 1.432 0.025 1.29e-02 6.01e+03 3.86e+00 bond pdb=" CA GLN A 587 " pdb=" C GLN A 587 " ideal model delta sigma weight residual 1.523 1.502 0.022 1.34e-02 5.57e+03 2.61e+00 bond pdb=" C LYS B 505 " pdb=" N LYS B 506 " ideal model delta sigma weight residual 1.331 1.369 -0.038 3.12e-02 1.03e+03 1.47e+00 bond pdb=" C LYS D 505 " pdb=" N LYS D 506 " ideal model delta sigma weight residual 1.331 1.368 -0.037 3.12e-02 1.03e+03 1.39e+00 ... (remaining 16786 not shown) Histogram of bond angle deviations from ideal: 96.92 - 105.39: 235 105.39 - 113.86: 9738 113.86 - 122.33: 10695 122.33 - 130.80: 2114 130.80 - 139.27: 55 Bond angle restraints: 22837 Sorted by residual: angle pdb=" CA GLY A 588 " pdb=" C GLY A 588 " pdb=" N CYS A 589 " ideal model delta sigma weight residual 114.96 96.92 18.04 1.15e+00 7.56e-01 2.46e+02 angle pdb=" O GLY A 588 " pdb=" C GLY A 588 " pdb=" N CYS A 589 " ideal model delta sigma weight residual 123.02 139.27 -16.25 1.98e+00 2.55e-01 6.73e+01 angle pdb=" C GLY A 588 " pdb=" N CYS A 589 " pdb=" CA CYS A 589 " ideal model delta sigma weight residual 121.32 104.45 16.87 2.10e+00 2.27e-01 6.45e+01 angle pdb=" N VAL C 795 " pdb=" CA VAL C 795 " pdb=" C VAL C 795 " ideal model delta sigma weight residual 113.53 108.09 5.44 9.80e-01 1.04e+00 3.08e+01 angle pdb=" N GLY C 423 " pdb=" CA GLY C 423 " pdb=" C GLY C 423 " ideal model delta sigma weight residual 110.56 115.27 -4.71 1.36e+00 5.41e-01 1.20e+01 ... (remaining 22832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.90: 8810 8.90 - 17.79: 669 17.79 - 26.69: 117 26.69 - 35.59: 79 35.59 - 44.48: 10 Dihedral angle restraints: 9685 sinusoidal: 3069 harmonic: 6616 Sorted by residual: dihedral pdb=" CA ALA B 522 " pdb=" C ALA B 522 " pdb=" N TYR B 523 " pdb=" CA TYR B 523 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ALA D 522 " pdb=" C ALA D 522 " pdb=" N TYR D 523 " pdb=" CA TYR D 523 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA PHE D 796 " pdb=" C PHE D 796 " pdb=" N TYR D 797 " pdb=" CA TYR D 797 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 9682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1834 0.033 - 0.066: 615 0.066 - 0.100: 179 0.100 - 0.133: 49 0.133 - 0.166: 3 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CA PRO C 520 " pdb=" N PRO C 520 " pdb=" C PRO C 520 " pdb=" CB PRO C 520 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA PRO A 520 " pdb=" N PRO A 520 " pdb=" C PRO A 520 " pdb=" CB PRO A 520 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA TYR B 797 " pdb=" N TYR B 797 " pdb=" C TYR B 797 " pdb=" CB TYR B 797 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 2677 not shown) Planarity restraints: 2866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 588 " 0.015 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C GLY A 588 " -0.064 2.00e-02 2.50e+03 pdb=" O GLY A 588 " 0.029 2.00e-02 2.50e+03 pdb=" N CYS A 589 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 606 " 0.016 2.00e-02 2.50e+03 1.49e-02 5.52e+00 pdb=" CG TRP A 606 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 606 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 606 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 606 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 606 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 606 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 606 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 606 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 606 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 606 " -0.016 2.00e-02 2.50e+03 1.45e-02 5.23e+00 pdb=" CG TRP C 606 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 606 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 606 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 606 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP C 606 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 606 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 606 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 606 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 606 " -0.002 2.00e-02 2.50e+03 ... (remaining 2863 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 357 2.68 - 3.24: 18212 3.24 - 3.79: 25129 3.79 - 4.35: 32939 4.35 - 4.90: 50779 Nonbonded interactions: 127416 Sorted by model distance: nonbonded pdb=" O PRO F 108 " pdb=" OG SER F 111 " model vdw 2.126 2.440 nonbonded pdb=" O PRO H 108 " pdb=" OG SER H 111 " model vdw 2.126 2.440 nonbonded pdb=" O GLN F 9 " pdb=" OG1 THR F 13 " model vdw 2.143 2.440 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.144 2.440 nonbonded pdb=" O GLN H 9 " pdb=" OG1 THR H 13 " model vdw 2.145 2.440 ... (remaining 127411 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 391 through 509 or (resid 510 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 518 or (resid 519 \ and (name N or name CA or name C or name O or name CB )) or resid 520 through 52 \ 4 or (resid 525 and (name N or name CA or name C or name O or name CB )) or resi \ d 526 or (resid 527 and (name N or name CA or name C or name O or name CB )) or \ resid 528 through 545 or (resid 546 and (name N or name CA or name C or name O o \ r name CB )) or resid 547 through 568 or (resid 569 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 through 584 or (resid 585 \ and (name N or name CA or name C or name O or name CB )) or resid 586 through 62 \ 4 or (resid 625 through 630 and (name N or name CA or name C or name O or name C \ B )) or resid 631 through 788 or (resid 789 and (name N or name CA or name C or \ name O or name CB )) or resid 790 through 806 or (resid 807 and (name N or name \ CA or name C or name O or name CB )) or resid 808 through 820 or (resid 821 thro \ ugh 825 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 391 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 507 through 566 or (resid 567 \ and (name N or name CA or name C or name O or name CB )) or resid 568 through 58 \ 6 or (resid 587 and (name N or name CA or name C or name O or name CB )) or resi \ d 588 through 632 or (resid 633 through 634 and (name N or name CA or name C or \ name O or name CB )) or resid 635 through 774 or resid 785 through 786 or (resid \ 787 and (name N or name CA or name C or name O or name CB )) or resid 788 throu \ gh 825)) selection = (chain 'C' and (resid 391 through 509 or (resid 510 through 511 and (name N or n \ ame CA or name C or name O or name CB )) or resid 512 through 518 or (resid 519 \ and (name N or name CA or name C or name O or name CB )) or resid 520 through 52 \ 4 or (resid 525 and (name N or name CA or name C or name O or name CB )) or resi \ d 526 or (resid 527 and (name N or name CA or name C or name O or name CB )) or \ resid 528 through 545 or (resid 546 and (name N or name CA or name C or name O o \ r name CB )) or resid 547 through 568 or (resid 569 through 571 and (name N or n \ ame CA or name C or name O or name CB )) or resid 572 through 584 or (resid 585 \ and (name N or name CA or name C or name O or name CB )) or resid 586 through 62 \ 4 or (resid 625 through 630 and (name N or name CA or name C or name O or name C \ B )) or resid 631 through 788 or (resid 789 and (name N or name CA or name C or \ name O or name CB )) or resid 790 through 806 or (resid 807 and (name N or name \ CA or name C or name O or name CB )) or resid 808 through 820 or (resid 821 thro \ ugh 825 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 391 through 504 or (resid 505 through 506 and (name N or n \ ame CA or name C or name O or name CB )) or resid 507 through 566 or (resid 567 \ and (name N or name CA or name C or name O or name CB )) or resid 568 through 58 \ 6 or (resid 587 and (name N or name CA or name C or name O or name CB )) or resi \ d 588 through 632 or (resid 633 through 634 and (name N or name CA or name C or \ name O or name CB )) or resid 635 through 774 or resid 785 through 786 or (resid \ 787 and (name N or name CA or name C or name O or name CB )) or resid 788 throu \ gh 825)) } ncs_group { reference = (chain 'E' and (resid 6 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 100 or (resid 101 throug \ h 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thro \ ugh 148 or (resid 149 through 151 and (name N or name CA or name C or name O or \ name CB )) or (resid 152 through 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 185 or (resid 186 through 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 199 or (resid 200 \ through 201 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 02 through 213)) selection = (chain 'F' and ((resid 6 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 25 or (resid 26 through 27 and (name N or nam \ e CA or name C or name O or name CB )) or resid 28 through 29 or (resid 30 throu \ gh 33 and (name N or name CA or name C or name O or name CB )) or resid 34 or (r \ esid 35 through 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 or (resid 57 through 61 and (name N or name CA or name C or name O or na \ me CB )) or resid 62 or (resid 63 through 66 and (name N or name CA or name C or \ name O or name CB )) or resid 67 or (resid 68 through 74 and (name N or name CA \ or name C or name O or name CB )) or resid 75 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or (resid 93 through 95 and (nam \ e N or name CA or name C or name O or name CB )) or resid 96 through 97 or (resi \ d 98 through 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 through 110 or (resid 111 through 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 or (resid 114 and (name N or name CA or n \ ame C or name O or name CB )) or resid 115 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or (resid 118 through 136 and (nam \ e N or name CA or name C or name O or name CB )) or resid 137 through 139 or (re \ sid 140 and (name N or name CA or name C or name O or name CB )) or resid 141 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 149 or (resid 150 through 151 and (name N or name CA or na \ me C or name O or name CB )) or resid 152 or (resid 153 through 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 or (resid 157 and (nam \ e N or name CA or name C or name O or name CB )) or resid 158 through 159 or (re \ sid 160 through 161 and (name N or name CA or name C or name O or name CB )) or \ resid 174 through 178 or (resid 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 through 190 or (resid 191 through 193 and (name N or n \ ame CA or name C or name O or name CB )) or resid 194 through 204 or (resid 205 \ through 213 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 6 through 22 or (resid 23 through 24 and (name N or name C \ A or name C or name O or name CB )) or resid 25 through 100 or (resid 101 throug \ h 105 and (name N or name CA or name C or name O or name CB )) or resid 106 thro \ ugh 148 or (resid 149 through 151 and (name N or name CA or name C or name O or \ name CB )) or (resid 152 through 155 and (name N or name CA or name C or name O \ or name CB )) or resid 156 through 185 or (resid 186 through 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 199 or (resid 200 \ through 201 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 02 through 213)) selection = (chain 'H' and ((resid 6 through 12 and (name N or name CA or name C or name O o \ r name CB )) or resid 13 or (resid 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 25 or (resid 26 through 27 and (name N or nam \ e CA or name C or name O or name CB )) or resid 28 through 29 or (resid 30 throu \ gh 33 and (name N or name CA or name C or name O or name CB )) or resid 34 or (r \ esid 35 through 37 and (name N or name CA or name C or name O or name CB )) or r \ esid 38 or (resid 57 through 61 and (name N or name CA or name C or name O or na \ me CB )) or resid 62 or (resid 63 through 66 and (name N or name CA or name C or \ name O or name CB )) or resid 67 or (resid 68 through 74 and (name N or name CA \ or name C or name O or name CB )) or resid 75 through 85 or (resid 86 and (name \ N or name CA or name C or name O or name CB )) or (resid 93 through 95 and (nam \ e N or name CA or name C or name O or name CB )) or resid 96 through 97 or (resi \ d 98 through 105 and (name N or name CA or name C or name O or name CB )) or res \ id 106 or (resid 107 and (name N or name CA or name C or name O or name CB )) or \ resid 108 through 110 or (resid 111 through 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 or (resid 114 and (name N or name CA or n \ ame C or name O or name CB )) or resid 115 through 116 or (resid 117 and (name N \ or name CA or name C or name O or name CB )) or (resid 118 through 136 and (nam \ e N or name CA or name C or name O or name CB )) or resid 137 through 139 or (re \ sid 140 and (name N or name CA or name C or name O or name CB )) or resid 141 th \ rough 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 149 or (resid 150 through 151 and (name N or name CA or na \ me C or name O or name CB )) or resid 152 or (resid 153 through 155 and (name N \ or name CA or name C or name O or name CB )) or resid 156 or (resid 157 and (nam \ e N or name CA or name C or name O or name CB )) or resid 158 through 159 or (re \ sid 160 through 161 and (name N or name CA or name C or name O or name CB )) or \ resid 174 through 178 or (resid 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 through 190 or (resid 191 through 193 and (name N or n \ ame CA or name C or name O or name CB )) or resid 194 through 204 or (resid 205 \ through 213 and (name N or name CA or name C or name O or name CB )))) } 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 95 5.16 5 C 10662 2.51 5 N 2666 2.21 5 O 3040 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.010 Extract box with map and model: 4.700 Check model and map are aligned: 0.250 Process input model: 44.840 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 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 : 0.004 0.206 16791 Z= 0.272 Angle : 0.666 18.045 22837 Z= 0.384 Chirality : 0.038 0.166 2680 Planarity : 0.004 0.048 2866 Dihedral : 7.574 44.482 5433 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.14), residues: 2262 helix: -2.21 (0.11), residues: 1280 sheet: -2.83 (0.38), residues: 140 loop : -3.22 (0.18), residues: 842 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 2.248 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 outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.2823 time to fit residues: 231.5063 Evaluate side-chains 333 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 205 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN F 199 HIS H 199 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B 764 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 16791 Z= 0.253 Angle : 0.634 11.786 22837 Z= 0.334 Chirality : 0.041 0.210 2680 Planarity : 0.004 0.035 2866 Dihedral : 4.554 26.794 2428 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2262 helix: 0.33 (0.14), residues: 1310 sheet: -2.24 (0.38), residues: 170 loop : -2.90 (0.20), residues: 782 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 447 time to evaluate : 1.926 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 outliers start: 4 outliers final: 0 residues processed: 449 average time/residue: 0.2458 time to fit residues: 172.3515 Evaluate side-chains 321 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 0.2980 chunk 170 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN D 764 ASN B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 16791 Z= 0.292 Angle : 0.657 11.964 22837 Z= 0.345 Chirality : 0.041 0.165 2680 Planarity : 0.004 0.037 2866 Dihedral : 4.701 29.632 2428 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 2262 helix: 1.09 (0.14), residues: 1304 sheet: -2.23 (0.40), residues: 156 loop : -2.77 (0.20), residues: 802 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 2.029 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 outliers start: 1 outliers final: 0 residues processed: 388 average time/residue: 0.2322 time to fit residues: 144.1903 Evaluate side-chains 298 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 0.0370 chunk 138 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 195 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS D 747 ASN B 435 HIS B 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16791 Z= 0.178 Angle : 0.590 10.775 22837 Z= 0.305 Chirality : 0.040 0.242 2680 Planarity : 0.003 0.040 2866 Dihedral : 4.388 27.366 2428 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2262 helix: 1.69 (0.15), residues: 1316 sheet: -1.82 (0.44), residues: 132 loop : -2.63 (0.20), residues: 814 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.980 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 outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2233 time to fit residues: 146.3783 Evaluate side-chains 307 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 16791 Z= 0.416 Angle : 0.781 11.119 22837 Z= 0.419 Chirality : 0.044 0.226 2680 Planarity : 0.004 0.038 2866 Dihedral : 5.176 32.827 2428 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.18), residues: 2262 helix: 0.89 (0.14), residues: 1306 sheet: -2.14 (0.36), residues: 186 loop : -2.62 (0.21), residues: 770 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 2.023 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 outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.2226 time to fit residues: 122.9902 Evaluate side-chains 256 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 587 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16791 Z= 0.211 Angle : 0.634 11.316 22837 Z= 0.329 Chirality : 0.042 0.172 2680 Planarity : 0.003 0.054 2866 Dihedral : 4.672 30.737 2428 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2262 helix: 1.49 (0.15), residues: 1314 sheet: -2.01 (0.36), residues: 182 loop : -2.47 (0.21), residues: 766 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 2.007 Fit side-chains 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: 378 average time/residue: 0.2202 time to fit residues: 136.0946 Evaluate side-chains 291 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 124 optimal weight: 0.0470 chunk 159 optimal weight: 8.9990 chunk 123 optimal weight: 20.0000 chunk 184 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 217 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 overall best weight: 1.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16791 Z= 0.189 Angle : 0.620 11.370 22837 Z= 0.319 Chirality : 0.041 0.277 2680 Planarity : 0.003 0.040 2866 Dihedral : 4.487 27.386 2428 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2262 helix: 1.70 (0.15), residues: 1322 sheet: -1.99 (0.39), residues: 166 loop : -2.44 (0.21), residues: 774 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 2.111 Fit side-chains 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: 370 average time/residue: 0.2228 time to fit residues: 135.3962 Evaluate side-chains 292 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 8.9990 chunk 86 optimal weight: 0.0470 chunk 130 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 171 optimal weight: 9.9990 chunk 198 optimal weight: 0.4980 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 435 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 16791 Z= 0.162 Angle : 0.605 11.252 22837 Z= 0.306 Chirality : 0.041 0.241 2680 Planarity : 0.003 0.041 2866 Dihedral : 4.276 25.626 2428 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.18), residues: 2262 helix: 1.96 (0.15), residues: 1312 sheet: -1.88 (0.39), residues: 148 loop : -2.42 (0.21), residues: 802 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 383 average time/residue: 0.2208 time to fit residues: 138.1559 Evaluate side-chains 314 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 183 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 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 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.076 16791 Z= 0.559 Angle : 0.952 11.669 22837 Z= 0.515 Chirality : 0.048 0.296 2680 Planarity : 0.005 0.040 2866 Dihedral : 5.816 33.502 2428 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 27.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.17), residues: 2262 helix: 0.25 (0.14), residues: 1316 sheet: -2.44 (0.39), residues: 134 loop : -2.68 (0.20), residues: 812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.831 Fit side-chains 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: 317 average time/residue: 0.2189 time to fit residues: 113.7194 Evaluate side-chains 247 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 149 optimal weight: 0.0870 chunk 225 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 714 GLN D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16791 Z= 0.194 Angle : 0.678 15.584 22837 Z= 0.345 Chirality : 0.043 0.247 2680 Planarity : 0.003 0.048 2866 Dihedral : 4.881 31.065 2428 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2262 helix: 1.38 (0.15), residues: 1312 sheet: -2.02 (0.36), residues: 174 loop : -2.51 (0.21), residues: 776 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4524 Ramachandran restraints generated. 2262 Oldfield, 0 Emsley, 2262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2209 time to fit residues: 131.4993 Evaluate side-chains 281 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.981 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 0.0770 chunk 179 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 157 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.070005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.056803 restraints weight = 78894.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.058345 restraints weight = 58201.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.059726 restraints weight = 40462.196| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 16791 Z= 0.184 Angle : 0.635 10.774 22837 Z= 0.326 Chirality : 0.041 0.215 2680 Planarity : 0.003 0.036 2866 Dihedral : 4.554 25.932 2428 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2262 helix: 1.69 (0.15), residues: 1312 sheet: -2.11 (0.38), residues: 144 loop : -2.41 (0.21), residues: 806 =============================================================================== Job complete usr+sys time: 3175.73 seconds wall clock time: 58 minutes 30.57 seconds (3510.57 seconds total)