Starting phenix.real_space_refine on Fri Sep 27 15:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/09_2024/5vot_8721_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/09_2024/5vot_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_8721/09_2024/5vot_8721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/09_2024/5vot_8721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/09_2024/5vot_8721_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vot_8721/09_2024/5vot_8721_neut.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 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. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.47, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 2.3 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: 2.00 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: 5.95 Time building geometry restraints manager: 5.51 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: 0.00 - 3.61: 22749 3.61 - 7.22: 77 7.22 - 10.83: 6 10.83 - 14.44: 2 14.44 - 18.04: 3 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 3.040 nonbonded pdb=" O PRO H 108 " pdb=" OG SER H 111 " model vdw 2.126 3.040 nonbonded pdb=" O GLN F 9 " pdb=" OG1 THR F 13 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLU A 705 " pdb=" OH TYR A 732 " model vdw 2.144 3.040 nonbonded pdb=" O GLN H 9 " pdb=" OG1 THR H 13 " model vdw 2.145 3.040 ... (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 Time spend for trying shortcut: 0.00 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 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: 1.150 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.810 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 % Allowed : 1.41 % Favored : 98.59 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 606 HIS 0.004 0.001 HIS F 199 PHE 0.015 0.002 PHE D 814 TYR 0.018 0.002 TYR B 797 ARG 0.004 0.001 ARG D 715 *********************** 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 : 1.922 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: A 424 TYR cc_start: 0.8281 (t80) cc_final: 0.8057 (t80) REVERT: A 527 MET cc_start: 0.8195 (mtm) cc_final: 0.7741 (mtp) REVERT: A 608 PHE cc_start: 0.8715 (t80) cc_final: 0.8412 (t80) REVERT: C 424 TYR cc_start: 0.8314 (t80) cc_final: 0.8086 (t80) REVERT: C 527 MET cc_start: 0.8164 (mtm) cc_final: 0.7771 (mtp) REVERT: C 608 PHE cc_start: 0.8718 (t80) cc_final: 0.8416 (t80) REVERT: C 659 PHE cc_start: 0.7367 (m-80) cc_final: 0.7166 (m-10) REVERT: C 703 LEU cc_start: 0.8685 (mt) cc_final: 0.8275 (mt) REVERT: D 405 TYR cc_start: 0.7775 (m-80) cc_final: 0.7280 (m-80) REVERT: D 425 CYS cc_start: 0.8765 (m) cc_final: 0.8169 (m) REVERT: D 483 LEU cc_start: 0.9119 (tp) cc_final: 0.8456 (tp) REVERT: D 498 LEU cc_start: 0.9405 (pp) cc_final: 0.9150 (pp) REVERT: D 503 MET cc_start: 0.7778 (ttm) cc_final: 0.7049 (ttm) REVERT: D 606 TRP cc_start: 0.8741 (m-10) cc_final: 0.8433 (m-10) REVERT: D 674 MET cc_start: 0.8148 (mtm) cc_final: 0.7909 (ptp) REVERT: D 750 VAL cc_start: 0.9237 (t) cc_final: 0.8967 (t) REVERT: E 155 VAL cc_start: 0.6311 (t) cc_final: 0.6052 (t) REVERT: F 141 PHE cc_start: -0.1535 (m-10) cc_final: -0.1843 (m-10) REVERT: F 151 ILE cc_start: 0.6200 (mt) cc_final: 0.5734 (mt) REVERT: F 195 VAL cc_start: 0.8985 (t) cc_final: 0.8758 (t) REVERT: G 195 VAL cc_start: 0.9027 (t) cc_final: 0.8808 (t) REVERT: H 141 PHE cc_start: -0.1533 (m-10) cc_final: -0.1846 (m-10) REVERT: H 151 ILE cc_start: 0.6209 (mt) cc_final: 0.5673 (mt) REVERT: H 195 VAL cc_start: 0.8968 (t) cc_final: 0.8759 (t) REVERT: B 405 TYR cc_start: 0.7789 (m-80) cc_final: 0.7474 (m-80) REVERT: B 425 CYS cc_start: 0.8579 (m) cc_final: 0.8236 (m) REVERT: B 483 LEU cc_start: 0.9105 (tp) cc_final: 0.8527 (tp) REVERT: B 498 LEU cc_start: 0.9397 (pp) cc_final: 0.9130 (pp) REVERT: B 503 MET cc_start: 0.7479 (ttm) cc_final: 0.6813 (ttm) REVERT: B 606 TRP cc_start: 0.8708 (m-10) cc_final: 0.8433 (m-10) REVERT: B 674 MET cc_start: 0.8134 (mtm) cc_final: 0.7931 (ptp) REVERT: B 750 VAL cc_start: 0.9227 (t) cc_final: 0.8975 (t) outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.2704 time to fit residues: 220.1932 Evaluate side-chains 344 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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: 2.9990 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN D 764 ASN F 199 HIS H 199 HIS ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN B 764 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16791 Z= 0.327 Angle : 0.691 12.410 22837 Z= 0.369 Chirality : 0.043 0.192 2680 Planarity : 0.004 0.045 2866 Dihedral : 4.767 29.712 2428 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.27 % Allowed : 3.15 % Favored : 96.58 % 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: -1.77 (0.17), residues: 2262 helix: 0.02 (0.14), residues: 1304 sheet: -2.30 (0.37), residues: 170 loop : -2.93 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 606 HIS 0.004 0.001 HIS D 412 PHE 0.046 0.003 PHE B 814 TYR 0.024 0.002 TYR B 797 ARG 0.003 0.000 ARG B 660 *********************** 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 437 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 433 time to evaluate : 2.028 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: A 424 TYR cc_start: 0.7986 (t80) cc_final: 0.7650 (t80) REVERT: A 463 MET cc_start: 0.7962 (mtm) cc_final: 0.7254 (mpp) REVERT: A 498 LEU cc_start: 0.9059 (pp) cc_final: 0.7882 (pp) REVERT: A 527 MET cc_start: 0.8191 (mtm) cc_final: 0.7441 (mtp) REVERT: A 732 TYR cc_start: 0.5419 (m-10) cc_final: 0.4155 (m-80) REVERT: A 760 ASP cc_start: 0.8700 (p0) cc_final: 0.8442 (t0) REVERT: C 424 TYR cc_start: 0.7971 (t80) cc_final: 0.7668 (t80) REVERT: C 463 MET cc_start: 0.7482 (mpp) cc_final: 0.7216 (mpp) REVERT: C 498 LEU cc_start: 0.9098 (pp) cc_final: 0.7944 (pp) REVERT: C 527 MET cc_start: 0.8169 (mtm) cc_final: 0.7464 (mtp) REVERT: C 732 TYR cc_start: 0.5230 (m-10) cc_final: 0.4132 (m-80) REVERT: D 425 CYS cc_start: 0.8732 (m) cc_final: 0.8494 (m) REVERT: D 485 ARG cc_start: 0.8775 (mtt180) cc_final: 0.8504 (mtt180) REVERT: D 809 VAL cc_start: 0.8490 (t) cc_final: 0.8160 (t) REVERT: E 22 SER cc_start: 0.8186 (t) cc_final: 0.7956 (p) REVERT: E 109 ILE cc_start: 0.6223 (pt) cc_final: 0.5977 (pt) REVERT: F 115 LEU cc_start: 0.4350 (tt) cc_final: 0.4044 (tp) REVERT: F 151 ILE cc_start: 0.6398 (mt) cc_final: 0.5675 (mt) REVERT: G 22 SER cc_start: 0.8154 (t) cc_final: 0.7942 (p) REVERT: G 109 ILE cc_start: 0.6254 (pt) cc_final: 0.6001 (pt) REVERT: H 115 LEU cc_start: 0.4361 (tt) cc_final: 0.4097 (tp) REVERT: H 151 ILE cc_start: 0.6297 (mt) cc_final: 0.5629 (mt) REVERT: B 405 TYR cc_start: 0.7469 (m-80) cc_final: 0.7121 (m-80) REVERT: B 425 CYS cc_start: 0.8889 (m) cc_final: 0.8627 (m) REVERT: B 485 ARG cc_start: 0.8823 (mtt180) cc_final: 0.8509 (mtt180) REVERT: B 613 ILE cc_start: 0.9684 (pt) cc_final: 0.9352 (mp) REVERT: B 809 VAL cc_start: 0.8667 (t) cc_final: 0.8461 (t) outliers start: 4 outliers final: 0 residues processed: 435 average time/residue: 0.2421 time to fit residues: 163.7498 Evaluate side-chains 328 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 139 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 222 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- 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 B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3538 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= 0.273 Angle : 0.650 11.345 22837 Z= 0.341 Chirality : 0.041 0.172 2680 Planarity : 0.004 0.040 2866 Dihedral : 4.696 30.639 2428 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % 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: -0.76 (0.18), residues: 2262 helix: 0.96 (0.14), residues: 1304 sheet: -2.09 (0.35), residues: 182 loop : -2.71 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 671 HIS 0.003 0.001 HIS D 412 PHE 0.024 0.002 PHE E 141 TYR 0.021 0.002 TYR B 523 ARG 0.003 0.000 ARG D 586 *********************** 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 413 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 412 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8113 (t80) cc_final: 0.7683 (t80) REVERT: A 463 MET cc_start: 0.7788 (mtm) cc_final: 0.7079 (mpp) REVERT: A 485 ARG cc_start: 0.8836 (mtt180) cc_final: 0.8629 (mtp180) REVERT: A 527 MET cc_start: 0.8123 (mtm) cc_final: 0.7857 (mtt) REVERT: C 424 TYR cc_start: 0.8032 (t80) cc_final: 0.7700 (t80) REVERT: C 503 MET cc_start: 0.7383 (ttm) cc_final: 0.7060 (ttm) REVERT: C 527 MET cc_start: 0.8113 (mtm) cc_final: 0.7849 (mtt) REVERT: D 405 TYR cc_start: 0.7873 (m-80) cc_final: 0.7629 (m-80) REVERT: D 425 CYS cc_start: 0.8707 (m) cc_final: 0.8434 (m) REVERT: D 485 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8320 (mtt180) REVERT: D 518 LEU cc_start: 0.8401 (pt) cc_final: 0.8193 (pp) REVERT: D 613 ILE cc_start: 0.9675 (pt) cc_final: 0.9469 (mp) REVERT: D 809 VAL cc_start: 0.8541 (t) cc_final: 0.8240 (t) REVERT: F 117 MET cc_start: 0.0772 (tpt) cc_final: 0.0264 (tpt) REVERT: F 136 LEU cc_start: 0.6753 (mm) cc_final: 0.6443 (mm) REVERT: F 151 ILE cc_start: 0.5620 (mt) cc_final: 0.4824 (mt) REVERT: H 117 MET cc_start: 0.0788 (tpt) cc_final: 0.0264 (tpt) REVERT: H 136 LEU cc_start: 0.6781 (mm) cc_final: 0.6534 (mm) REVERT: H 151 ILE cc_start: 0.5567 (mt) cc_final: 0.4777 (mt) REVERT: B 425 CYS cc_start: 0.8894 (m) cc_final: 0.8642 (m) REVERT: B 463 MET cc_start: 0.7208 (mtt) cc_final: 0.6944 (mmm) REVERT: B 485 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8331 (mtt180) outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.2338 time to fit residues: 152.8796 Evaluate side-chains 317 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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: 1.9990 chunk 154 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 98 optimal weight: 0.0370 chunk 138 optimal weight: 10.0000 chunk 206 optimal weight: 0.0970 chunk 218 optimal weight: 8.9990 chunk 107 optimal weight: 0.0060 chunk 195 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 overall best weight: 0.3472 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16791 Z= 0.136 Angle : 0.576 10.764 22837 Z= 0.291 Chirality : 0.041 0.253 2680 Planarity : 0.003 0.044 2866 Dihedral : 4.275 25.985 2428 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 0.23 (0.18), residues: 2262 helix: 1.88 (0.15), residues: 1316 sheet: -1.85 (0.42), residues: 132 loop : -2.58 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 605 HIS 0.003 0.001 HIS D 435 PHE 0.029 0.001 PHE G 141 TYR 0.024 0.001 TYR A 732 ARG 0.007 0.000 ARG A 715 *********************** 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 427 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 427 time to evaluate : 1.885 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: A 424 TYR cc_start: 0.7887 (t80) cc_final: 0.7582 (t80) REVERT: A 491 PHE cc_start: 0.7926 (m-80) cc_final: 0.7121 (m-80) REVERT: A 533 TYR cc_start: 0.8731 (t80) cc_final: 0.7931 (t80) REVERT: A 541 PHE cc_start: 0.7780 (t80) cc_final: 0.6523 (t80) REVERT: C 424 TYR cc_start: 0.7770 (t80) cc_final: 0.7484 (t80) REVERT: C 503 MET cc_start: 0.7367 (ttm) cc_final: 0.7121 (ptt) REVERT: C 527 MET cc_start: 0.7786 (mtm) cc_final: 0.7536 (mtt) REVERT: C 528 CYS cc_start: 0.8979 (m) cc_final: 0.8749 (m) REVERT: C 533 TYR cc_start: 0.8663 (t80) cc_final: 0.8016 (t80) REVERT: C 541 PHE cc_start: 0.7774 (t80) cc_final: 0.6526 (t80) REVERT: D 425 CYS cc_start: 0.8564 (m) cc_final: 0.8323 (m) REVERT: D 463 MET cc_start: 0.7138 (mtm) cc_final: 0.6815 (mtt) REVERT: D 479 LEU cc_start: 0.8865 (tp) cc_final: 0.8468 (tp) REVERT: D 518 LEU cc_start: 0.7899 (pt) cc_final: 0.7607 (pp) REVERT: D 708 MET cc_start: 0.7435 (mmt) cc_final: 0.6755 (mmt) REVERT: F 151 ILE cc_start: 0.7015 (mt) cc_final: 0.6734 (mt) REVERT: H 151 ILE cc_start: 0.6928 (mt) cc_final: 0.6682 (mt) REVERT: B 463 MET cc_start: 0.6813 (mtt) cc_final: 0.6406 (mtt) REVERT: B 479 LEU cc_start: 0.8663 (tp) cc_final: 0.8267 (tp) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.2246 time to fit residues: 152.7429 Evaluate side-chains 328 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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: 2.9990 chunk 124 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** 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: 0.7422 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16791 Z= 0.359 Angle : 0.729 10.763 22837 Z= 0.390 Chirality : 0.044 0.213 2680 Planarity : 0.004 0.041 2866 Dihedral : 4.933 31.129 2428 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: -0.44 (0.18), residues: 2262 helix: 1.17 (0.14), residues: 1316 sheet: -1.92 (0.41), residues: 152 loop : -2.53 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 578 HIS 0.004 0.001 HIS F 199 PHE 0.030 0.003 PHE F 142 TYR 0.023 0.002 TYR D 797 ARG 0.005 0.001 ARG A 715 *********************** 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 359 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8100 (t80) cc_final: 0.7608 (t80) REVERT: A 503 MET cc_start: 0.7473 (ptm) cc_final: 0.7256 (ptt) REVERT: A 704 LEU cc_start: 0.8824 (pp) cc_final: 0.8426 (tp) REVERT: C 503 MET cc_start: 0.7565 (ttm) cc_final: 0.7292 (ttm) REVERT: C 527 MET cc_start: 0.8222 (mtm) cc_final: 0.7275 (mtp) REVERT: D 517 PHE cc_start: 0.8268 (t80) cc_final: 0.7853 (t80) REVERT: D 518 LEU cc_start: 0.8843 (pt) cc_final: 0.8575 (pt) REVERT: G 195 VAL cc_start: 0.9246 (t) cc_final: 0.9035 (t) REVERT: G 200 MET cc_start: 0.9691 (ttm) cc_final: 0.9488 (mmm) REVERT: H 140 ILE cc_start: 0.3163 (pt) cc_final: 0.2275 (pt) REVERT: H 192 MET cc_start: 0.8693 (ttt) cc_final: 0.8469 (ttt) REVERT: B 425 CYS cc_start: 0.8746 (m) cc_final: 0.8488 (m) REVERT: B 479 LEU cc_start: 0.8429 (tp) cc_final: 0.8181 (tp) REVERT: B 517 PHE cc_start: 0.8457 (t80) cc_final: 0.7995 (t80) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.2221 time to fit residues: 128.7735 Evaluate side-chains 285 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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: 3.9990 chunk 196 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 218 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16791 Z= 0.168 Angle : 0.612 11.046 22837 Z= 0.315 Chirality : 0.041 0.172 2680 Planarity : 0.003 0.057 2866 Dihedral : 4.470 28.327 2428 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 0.11 (0.18), residues: 2262 helix: 1.68 (0.15), residues: 1320 sheet: -1.71 (0.44), residues: 132 loop : -2.47 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 605 HIS 0.001 0.000 HIS D 435 PHE 0.032 0.002 PHE E 141 TYR 0.016 0.001 TYR D 702 ARG 0.013 0.001 ARG C 715 *********************** 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 380 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 2.041 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: A 671 TRP cc_start: 0.6984 (t-100) cc_final: 0.6691 (t-100) REVERT: A 674 MET cc_start: 0.6540 (ptp) cc_final: 0.6175 (ptp) REVERT: A 704 LEU cc_start: 0.8544 (pp) cc_final: 0.8270 (tp) REVERT: C 424 TYR cc_start: 0.7313 (t80) cc_final: 0.6935 (t80) REVERT: C 503 MET cc_start: 0.7353 (ttm) cc_final: 0.7063 (ptm) REVERT: C 527 MET cc_start: 0.8031 (mtm) cc_final: 0.7718 (mtt) REVERT: C 528 CYS cc_start: 0.8892 (m) cc_final: 0.8647 (m) REVERT: C 541 PHE cc_start: 0.7871 (t80) cc_final: 0.6690 (t80) REVERT: C 755 GLU cc_start: 0.8061 (pm20) cc_final: 0.7704 (pm20) REVERT: D 405 TYR cc_start: 0.7771 (m-80) cc_final: 0.7513 (m-80) REVERT: D 425 CYS cc_start: 0.8778 (m) cc_final: 0.8564 (m) REVERT: D 589 CYS cc_start: 0.8616 (t) cc_final: 0.8369 (t) REVERT: D 708 MET cc_start: 0.7480 (mmt) cc_final: 0.7087 (mmt) REVERT: G 195 VAL cc_start: 0.9161 (t) cc_final: 0.8948 (t) REVERT: H 115 LEU cc_start: 0.4155 (tp) cc_final: 0.3932 (tp) REVERT: H 117 MET cc_start: 0.0926 (tpt) cc_final: 0.0724 (tpt) REVERT: B 425 CYS cc_start: 0.8617 (m) cc_final: 0.8205 (m) REVERT: B 479 LEU cc_start: 0.8353 (tp) cc_final: 0.7760 (tp) REVERT: B 517 PHE cc_start: 0.8161 (t80) cc_final: 0.7699 (t80) REVERT: B 589 CYS cc_start: 0.8515 (t) cc_final: 0.8305 (t) outliers start: 0 outliers final: 0 residues processed: 380 average time/residue: 0.2156 time to fit residues: 133.4170 Evaluate side-chains 311 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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: 5.9990 chunk 24 optimal weight: 10.0000 chunk 124 optimal weight: 0.0370 chunk 159 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 217 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** 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: 0.7380 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16791 Z= 0.287 Angle : 0.677 11.103 22837 Z= 0.357 Chirality : 0.042 0.158 2680 Planarity : 0.004 0.046 2866 Dihedral : 4.701 29.956 2428 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % 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: -0.18 (0.18), residues: 2262 helix: 1.41 (0.14), residues: 1316 sheet: -1.73 (0.45), residues: 132 loop : -2.52 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 605 HIS 0.005 0.001 HIS H 199 PHE 0.029 0.002 PHE H 142 TYR 0.023 0.002 TYR C 732 ARG 0.004 0.000 ARG A 715 *********************** 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 358 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 1.779 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: A 533 TYR cc_start: 0.8814 (t80) cc_final: 0.8537 (t80) REVERT: A 671 TRP cc_start: 0.7214 (t-100) cc_final: 0.6760 (t-100) REVERT: C 527 MET cc_start: 0.8253 (mtm) cc_final: 0.7961 (mtt) REVERT: C 533 TYR cc_start: 0.8869 (t80) cc_final: 0.8529 (t80) REVERT: D 496 MET cc_start: 0.7684 (tpp) cc_final: 0.7462 (tpp) REVERT: D 517 PHE cc_start: 0.8113 (t80) cc_final: 0.7805 (t80) REVERT: D 541 PHE cc_start: 0.8452 (t80) cc_final: 0.8163 (t80) REVERT: D 708 MET cc_start: 0.7613 (mmt) cc_final: 0.7207 (mmt) REVERT: H 117 MET cc_start: 0.0363 (tpt) cc_final: 0.0004 (tpt) REVERT: H 151 ILE cc_start: 0.7188 (mt) cc_final: 0.6918 (mt) REVERT: B 425 CYS cc_start: 0.8458 (m) cc_final: 0.8254 (m) REVERT: B 496 MET cc_start: 0.7650 (tpp) cc_final: 0.7372 (tpp) REVERT: B 589 CYS cc_start: 0.8624 (t) cc_final: 0.8414 (t) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.2122 time to fit residues: 123.2072 Evaluate side-chains 297 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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: 3.9990 chunk 86 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 138 optimal weight: 9.9990 chunk 148 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 198 optimal weight: 0.2980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS B 435 HIS ** 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: 0.7309 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16791 Z= 0.187 Angle : 0.625 11.581 22837 Z= 0.322 Chirality : 0.041 0.257 2680 Planarity : 0.003 0.052 2866 Dihedral : 4.469 28.615 2428 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 0.15 (0.18), residues: 2262 helix: 1.68 (0.15), residues: 1318 sheet: -1.89 (0.40), residues: 152 loop : -2.34 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 767 HIS 0.005 0.001 HIS D 435 PHE 0.039 0.002 PHE F 141 TYR 0.021 0.001 TYR C 732 ARG 0.004 0.000 ARG D 586 *********************** 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 382 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 1.854 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: A 424 TYR cc_start: 0.7558 (t80) cc_final: 0.7343 (t80) REVERT: A 425 CYS cc_start: 0.8346 (m) cc_final: 0.8144 (m) REVERT: A 491 PHE cc_start: 0.7933 (m-80) cc_final: 0.7225 (m-80) REVERT: A 533 TYR cc_start: 0.8864 (t80) cc_final: 0.8366 (t80) REVERT: A 541 PHE cc_start: 0.7866 (t80) cc_final: 0.6650 (t80) REVERT: A 671 TRP cc_start: 0.7229 (t-100) cc_final: 0.6674 (t-100) REVERT: A 704 LEU cc_start: 0.8568 (pp) cc_final: 0.8194 (tp) REVERT: C 402 GLU cc_start: 0.6440 (mm-30) cc_final: 0.6179 (mm-30) REVERT: C 424 TYR cc_start: 0.7384 (t80) cc_final: 0.7027 (t80) REVERT: C 503 MET cc_start: 0.7657 (ttp) cc_final: 0.7057 (ptt) REVERT: C 527 MET cc_start: 0.8106 (mtm) cc_final: 0.7678 (mtt) REVERT: C 533 TYR cc_start: 0.8877 (t80) cc_final: 0.8406 (t80) REVERT: C 541 PHE cc_start: 0.7934 (t80) cc_final: 0.6722 (t80) REVERT: C 799 LEU cc_start: 0.9115 (tp) cc_final: 0.8856 (tp) REVERT: D 517 PHE cc_start: 0.8110 (t80) cc_final: 0.7585 (t80) REVERT: D 518 LEU cc_start: 0.8470 (pt) cc_final: 0.7984 (pp) REVERT: D 581 LEU cc_start: 0.9113 (tp) cc_final: 0.8841 (tt) REVERT: D 589 CYS cc_start: 0.8577 (t) cc_final: 0.8369 (t) REVERT: D 708 MET cc_start: 0.7522 (mmt) cc_final: 0.7023 (mmt) REVERT: F 115 LEU cc_start: 0.4542 (tp) cc_final: 0.4321 (tp) REVERT: F 136 LEU cc_start: 0.6366 (mm) cc_final: 0.5968 (mm) REVERT: F 151 ILE cc_start: 0.7267 (mt) cc_final: 0.7047 (mt) REVERT: B 425 CYS cc_start: 0.8453 (m) cc_final: 0.8242 (m) REVERT: B 479 LEU cc_start: 0.8649 (tp) cc_final: 0.8404 (tp) REVERT: B 517 PHE cc_start: 0.8168 (t80) cc_final: 0.7756 (t80) REVERT: B 581 LEU cc_start: 0.9024 (tp) cc_final: 0.8767 (tt) REVERT: B 589 CYS cc_start: 0.8542 (t) cc_final: 0.8303 (t) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.2287 time to fit residues: 143.5342 Evaluate side-chains 313 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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: 1.9990 chunk 190 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 159 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 191 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** 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: 0.7451 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16791 Z= 0.400 Angle : 0.788 11.080 22837 Z= 0.423 Chirality : 0.044 0.268 2680 Planarity : 0.004 0.047 2866 Dihedral : 5.118 32.059 2428 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: -0.56 (0.18), residues: 2262 helix: 1.03 (0.14), residues: 1312 sheet: -1.92 (0.44), residues: 132 loop : -2.50 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 578 HIS 0.006 0.002 HIS H 199 PHE 0.031 0.003 PHE A 607 TYR 0.029 0.002 TYR D 797 ARG 0.004 0.001 ARG A 715 *********************** 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 344 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 1.736 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: A 425 CYS cc_start: 0.8565 (m) cc_final: 0.8295 (m) REVERT: A 491 PHE cc_start: 0.8251 (m-80) cc_final: 0.7357 (m-80) REVERT: A 533 TYR cc_start: 0.8820 (t80) cc_final: 0.8413 (t80) REVERT: A 751 LEU cc_start: 0.9346 (pp) cc_final: 0.8974 (pp) REVERT: A 755 GLU cc_start: 0.8350 (pm20) cc_final: 0.7870 (pm20) REVERT: C 527 MET cc_start: 0.8364 (mtm) cc_final: 0.8135 (mtt) REVERT: C 533 TYR cc_start: 0.8848 (t80) cc_final: 0.8379 (t80) REVERT: C 659 PHE cc_start: 0.7454 (m-10) cc_final: 0.7238 (m-10) REVERT: D 405 TYR cc_start: 0.7607 (m-80) cc_final: 0.7357 (m-80) REVERT: D 503 MET cc_start: 0.6839 (ttm) cc_final: 0.6616 (ttm) REVERT: D 708 MET cc_start: 0.7563 (mmt) cc_final: 0.7205 (mmt) REVERT: D 812 ILE cc_start: 0.8233 (mt) cc_final: 0.7999 (tp) REVERT: F 115 LEU cc_start: 0.4614 (tp) cc_final: 0.4322 (tp) REVERT: F 136 LEU cc_start: 0.5956 (mm) cc_final: 0.5262 (mm) REVERT: F 191 GLU cc_start: 0.9021 (mp0) cc_final: 0.8815 (mp0) REVERT: H 115 LEU cc_start: 0.4635 (tp) cc_final: 0.4319 (tp) REVERT: H 140 ILE cc_start: 0.3686 (pt) cc_final: 0.3374 (pt) REVERT: B 425 CYS cc_start: 0.8422 (m) cc_final: 0.8176 (m) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.2171 time to fit residues: 121.4785 Evaluate side-chains 270 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.938 ------------------------------------------------------------------------------- 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: 0.8980 chunk 101 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS ** 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: 0.7329 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16791 Z= 0.197 Angle : 0.664 11.441 22837 Z= 0.344 Chirality : 0.042 0.269 2680 Planarity : 0.004 0.061 2866 Dihedral : 4.667 30.552 2428 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.05 (0.18), residues: 2262 helix: 1.49 (0.15), residues: 1314 sheet: -1.84 (0.44), residues: 132 loop : -2.37 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 178 HIS 0.005 0.001 HIS D 435 PHE 0.034 0.002 PHE A 607 TYR 0.020 0.002 TYR C 732 ARG 0.004 0.000 ARG D 586 ********************** 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 : 1.916 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: A 425 CYS cc_start: 0.8422 (m) cc_final: 0.8196 (m) REVERT: A 533 TYR cc_start: 0.8833 (t80) cc_final: 0.8388 (t80) REVERT: A 541 PHE cc_start: 0.7671 (t80) cc_final: 0.6383 (t80) REVERT: A 751 LEU cc_start: 0.9126 (pp) cc_final: 0.8798 (pp) REVERT: A 755 GLU cc_start: 0.8335 (pm20) cc_final: 0.7795 (pm20) REVERT: C 424 TYR cc_start: 0.7415 (t80) cc_final: 0.7127 (t80) REVERT: C 799 LEU cc_start: 0.9058 (tp) cc_final: 0.8810 (tp) REVERT: D 405 TYR cc_start: 0.7563 (m-80) cc_final: 0.7308 (m-80) REVERT: D 517 PHE cc_start: 0.8212 (t80) cc_final: 0.7402 (t80) REVERT: D 581 LEU cc_start: 0.9160 (tp) cc_final: 0.8892 (tt) REVERT: D 589 CYS cc_start: 0.8442 (t) cc_final: 0.8239 (t) REVERT: D 708 MET cc_start: 0.7383 (mmt) cc_final: 0.6995 (mmt) REVERT: F 21 PHE cc_start: 0.7288 (t80) cc_final: 0.7052 (t80) REVERT: F 191 GLU cc_start: 0.8943 (mp0) cc_final: 0.8718 (mp0) REVERT: H 21 PHE cc_start: 0.7366 (t80) cc_final: 0.7020 (t80) REVERT: H 151 ILE cc_start: 0.7346 (mt) cc_final: 0.7019 (mt) REVERT: B 425 CYS cc_start: 0.8401 (m) cc_final: 0.8189 (m) REVERT: B 479 LEU cc_start: 0.8710 (tp) cc_final: 0.8489 (tp) REVERT: B 517 PHE cc_start: 0.8304 (t80) cc_final: 0.8025 (t80) REVERT: B 581 LEU cc_start: 0.8941 (tp) cc_final: 0.8721 (tt) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2205 time to fit residues: 130.3252 Evaluate side-chains 291 residues out of total 1930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.900 ------------------------------------------------------------------------------- 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: 0.0970 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 179 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 0.0020 chunk 157 optimal weight: 20.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS B 435 HIS ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.058779 restraints weight = 76511.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060396 restraints weight = 55114.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.061914 restraints weight = 38215.552| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16791 Z= 0.155 Angle : 0.644 12.863 22837 Z= 0.324 Chirality : 0.042 0.263 2680 Planarity : 0.003 0.055 2866 Dihedral : 4.343 26.082 2428 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.28 (0.18), residues: 2262 helix: 1.82 (0.15), residues: 1306 sheet: -1.82 (0.42), residues: 136 loop : -2.30 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 605 HIS 0.006 0.001 HIS D 435 PHE 0.033 0.002 PHE A 607 TYR 0.018 0.001 TYR D 702 ARG 0.004 0.000 ARG D 586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3414.29 seconds wall clock time: 61 minutes 52.19 seconds (3712.19 seconds total)