Starting phenix.real_space_refine (version: dev) on Wed Apr 6 21:55:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/04_2022/6whr_21673.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/04_2022/6whr_21673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/04_2022/6whr_21673.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/04_2022/6whr_21673.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/04_2022/6whr_21673.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6whr_21673/04_2022/6whr_21673.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.684 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 23370 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5870 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 539 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 7, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 304 Chain: "B" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5717 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 7, 'PHE:plan': 8, 'GLU:plan': 25, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 343 Chain: "C" Number of atoms: 5870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 799, 5870 Classifications: {'peptide': 799} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 35, 'TRANS': 763} Chain breaks: 3 Unresolved non-hydrogen bonds: 454 Unresolved non-hydrogen angles: 539 Unresolved non-hydrogen dihedrals: 393 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 7, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 304 Chain: "D" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5717 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 498 Unresolved non-hydrogen angles: 612 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 7, 'PHE:plan': 8, 'GLU:plan': 25, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 343 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.94, per 1000 atoms: 0.55 Number of scatterers: 23370 At special positions: 0 Unit cell: (143.85, 149.33, 180.84, 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 130 16.00 O 4428 8.00 N 3828 7.00 C 14984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.05 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.04 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.05 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.05 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.04 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.05 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1001 " - " ASN A 224 " " NAG A1002 " - " ASN A 297 " " NAG B 903 " - " ASN B 542 " " NAG B 904 " - " ASN B 341 " " NAG B 905 " - " ASN B 491 " " NAG C1001 " - " ASN C 224 " " NAG C1002 " - " ASN C 297 " " NAG D 903 " - " ASN D 542 " " NAG D 904 " - " ASN D 341 " " NAG D 905 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 10.15 Conformation dependent library (CDL) restraints added in 3.6 seconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5912 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 30 sheets defined 41.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.656A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.772A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.965A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.029A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 157 removed outlier: 5.176A pdb=" N MET A 155 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 157 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.668A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.694A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.514A pdb=" N ALA A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 297 through 315 removed outlier: 4.004A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 479 through 490 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.562A pdb=" N GLU A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.982A pdb=" N TYR A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 548' Processing helix chain 'A' and resid 576 through 580 removed outlier: 4.373A pdb=" N GLN A 580 " --> pdb=" O GLN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 605 removed outlier: 4.330A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 637 removed outlier: 3.895A pdb=" N TRP A 629 " --> pdb=" O SER A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 3.687A pdb=" N ILE A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.608A pdb=" N ARG A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 720 through 729 removed outlier: 3.984A pdb=" N LYS A 729 " --> pdb=" O ARG A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 743 Processing helix chain 'A' and resid 754 through 764 removed outlier: 5.286A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 801 removed outlier: 3.517A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 removed outlier: 3.681A pdb=" N ASP A 810 " --> pdb=" O MET A 806 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.813A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.954A pdb=" N LYS B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 4.314A pdb=" N VAL B 64 " --> pdb=" O HIS B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 77 through 93 Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.855A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.876A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.668A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 234 through 248 removed outlier: 3.557A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 310 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 460 through 473 Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.986A pdb=" N GLU B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 578 removed outlier: 3.619A pdb=" N GLU B 578 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 4.311A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 654 Processing helix chain 'B' and resid 668 through 672 Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.849A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 741 through 743 No H-bonds generated for 'chain 'B' and resid 741 through 743' Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.549A pdb=" N ASP B 786 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.637A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 843 removed outlier: 3.805A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE B 837 " --> pdb=" O LEU B 833 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 839 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.657A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 removed outlier: 3.773A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.964A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 143 through 148 removed outlier: 4.028A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 157 removed outlier: 5.176A pdb=" N MET C 155 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 157 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 removed outlier: 3.668A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.694A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 260 removed outlier: 3.514A pdb=" N ALA C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 Processing helix chain 'C' and resid 297 through 315 removed outlier: 4.004A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 346 Processing helix chain 'C' and resid 479 through 490 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.563A pdb=" N GLU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 548 removed outlier: 3.981A pdb=" N TYR C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 548 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 548' Processing helix chain 'C' and resid 576 through 580 removed outlier: 4.372A pdb=" N GLN C 580 " --> pdb=" O GLN C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 605 removed outlier: 4.330A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 637 removed outlier: 3.896A pdb=" N TRP C 629 " --> pdb=" O SER C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 3.688A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.608A pdb=" N ARG C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.983A pdb=" N LYS C 729 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 743 Processing helix chain 'C' and resid 754 through 764 removed outlier: 5.287A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 801 removed outlier: 3.517A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 removed outlier: 3.682A pdb=" N ASP C 810 " --> pdb=" O MET C 806 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS C 811 " --> pdb=" O GLU C 807 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 812 " --> pdb=" O ASP C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 862 removed outlier: 4.813A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.954A pdb=" N LYS D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 4.314A pdb=" N VAL D 64 " --> pdb=" O HIS D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 77 through 93 Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.854A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.876A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 removed outlier: 3.668A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 234 through 248 removed outlier: 3.556A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 310 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 460 through 473 Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.986A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.619A pdb=" N GLU D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 4.311A pdb=" N ILE D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 654 Processing helix chain 'D' and resid 668 through 672 Processing helix chain 'D' and resid 690 through 699 removed outlier: 3.851A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 708 through 710 No H-bonds generated for 'chain 'D' and resid 708 through 710' Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.549A pdb=" N ASP D 786 " --> pdb=" O GLN D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.637A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU D 793 " --> pdb=" O MET D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 843 removed outlier: 3.805A pdb=" N ALA D 828 " --> pdb=" O MET D 824 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET D 829 " --> pdb=" O LEU D 825 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 837 " --> pdb=" O LEU D 833 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER D 838 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU D 839 " --> pdb=" O THR D 835 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.449A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 216 removed outlier: 6.445A pdb=" N LEU A 165 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 166 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 7.357A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 422 through 423 removed outlier: 3.773A pdb=" N THR A 423 " --> pdb=" O HIS A 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 434 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 removed outlier: 4.433A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 753 removed outlier: 3.631A pdb=" N VAL A 563 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL A 768 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 69 removed outlier: 3.631A pdb=" N ILE B 37 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 199 through 204 removed outlier: 8.097A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 280 removed outlier: 6.882A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 341 through 344 Processing sheet with id=AB3, first strand: chain 'B' and resid 475 through 477 removed outlier: 8.964A pdb=" N MET B 508 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER B 407 " --> pdb=" O MET B 508 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB6, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.853A pdb=" N ALA B 728 " --> pdb=" O GLY B 684 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA B 758 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.448A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 215 through 216 removed outlier: 6.445A pdb=" N LEU C 165 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU C 166 " --> pdb=" O SER C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 288 through 292 removed outlier: 7.356A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 422 through 423 removed outlier: 3.773A pdb=" N THR C 423 " --> pdb=" O HIS C 498 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 430 through 434 Processing sheet with id=AC3, first strand: chain 'C' and resid 508 through 511 removed outlier: 4.434A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 750 through 753 removed outlier: 3.631A pdb=" N VAL C 563 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 768 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 66 through 69 removed outlier: 3.631A pdb=" N ILE D 37 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 9.590A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 199 through 204 removed outlier: 8.098A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 278 through 280 removed outlier: 6.882A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 341 through 344 Processing sheet with id=AC9, first strand: chain 'D' and resid 475 through 477 removed outlier: 8.964A pdb=" N MET D 508 " --> pdb=" O HIS D 405 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER D 407 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 419 through 420 Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.854A pdb=" N ALA D 728 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) 926 hydrogen bonds defined for protein. 2658 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: 7.83 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6131 1.33 - 1.46: 6905 1.46 - 1.59: 10604 1.59 - 1.72: 0 1.72 - 1.85: 218 Bond restraints: 23858 Sorted by residual: bond pdb=" CA ALA A 755 " pdb=" C ALA A 755 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.79e+01 bond pdb=" CA ALA C 755 " pdb=" C ALA C 755 " ideal model delta sigma weight residual 1.523 1.413 0.110 1.34e-02 5.57e+03 6.75e+01 bond pdb=" CA SER D 520 " pdb=" C SER D 520 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.34e-02 5.57e+03 4.43e+01 bond pdb=" CA SER B 520 " pdb=" C SER B 520 " ideal model delta sigma weight residual 1.523 1.435 0.089 1.34e-02 5.57e+03 4.37e+01 bond pdb=" CA MET B 789 " pdb=" C MET B 789 " ideal model delta sigma weight residual 1.524 1.404 0.120 2.25e-02 1.98e+03 2.83e+01 ... (remaining 23853 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.65: 439 104.65 - 112.05: 12775 112.05 - 119.44: 7627 119.44 - 126.83: 11445 126.83 - 134.23: 300 Bond angle restraints: 32586 Sorted by residual: angle pdb=" C LYS D 747 " pdb=" N LEU D 748 " pdb=" CA LEU D 748 " ideal model delta sigma weight residual 121.64 114.05 7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" C LYS B 747 " pdb=" N LEU B 748 " pdb=" CA LEU B 748 " ideal model delta sigma weight residual 121.64 114.09 7.55 1.20e+00 6.94e-01 3.96e+01 angle pdb=" C PHE D 529 " pdb=" CA PHE D 529 " pdb=" CB PHE D 529 " ideal model delta sigma weight residual 111.39 103.02 8.37 1.59e+00 3.96e-01 2.77e+01 angle pdb=" C PHE B 529 " pdb=" CA PHE B 529 " pdb=" CB PHE B 529 " ideal model delta sigma weight residual 111.39 103.07 8.32 1.59e+00 3.96e-01 2.73e+01 angle pdb=" C LEU C 676 " pdb=" N VAL C 677 " pdb=" CA VAL C 677 " ideal model delta sigma weight residual 122.35 116.84 5.51 1.18e+00 7.18e-01 2.18e+01 ... (remaining 32581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 12958 21.50 - 42.99: 921 42.99 - 64.48: 130 64.48 - 85.98: 27 85.98 - 107.47: 10 Dihedral angle restraints: 14046 sinusoidal: 4886 harmonic: 9160 Sorted by residual: dihedral pdb=" CA CYS D 429 " pdb=" C CYS D 429 " pdb=" N MET D 430 " pdb=" CA MET D 430 " ideal model delta harmonic sigma weight residual 180.00 132.00 48.00 0 5.00e+00 4.00e-02 9.22e+01 dihedral pdb=" CA CYS B 429 " pdb=" C CYS B 429 " pdb=" N MET B 430 " pdb=" CA MET B 430 " ideal model delta harmonic sigma weight residual 180.00 132.06 47.94 0 5.00e+00 4.00e-02 9.19e+01 dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -165.58 79.58 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 14043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3910 0.321 - 0.643: 2 0.643 - 0.964: 0 0.964 - 1.286: 0 1.286 - 1.607: 2 Chirality restraints: 3914 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.79 -1.61 2.00e-02 2.50e+03 6.46e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.79 -1.61 2.00e-02 2.50e+03 6.45e+03 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 224 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 9.03e+00 ... (remaining 3911 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 632 " -0.023 2.00e-02 2.50e+03 1.52e-02 5.81e+00 pdb=" CG TRP A 632 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 632 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 632 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 632 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 632 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 632 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 632 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 632 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 632 " 0.023 2.00e-02 2.50e+03 1.52e-02 5.81e+00 pdb=" CG TRP C 632 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP C 632 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP C 632 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 632 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 632 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 632 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 632 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 632 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 632 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 547 " 0.001 2.00e-02 2.50e+03 1.61e-02 5.17e+00 pdb=" CG TYR C 547 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 547 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 547 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR C 547 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 547 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 547 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 547 " -0.003 2.00e-02 2.50e+03 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 497 2.55 - 3.14: 24171 3.14 - 3.73: 35745 3.73 - 4.31: 46420 4.31 - 4.90: 70640 Nonbonded interactions: 177473 Sorted by model distance: nonbonded pdb=" OG1 THR A 446 " pdb=" OD1 ASN A 448 " model vdw 1.968 2.440 nonbonded pdb=" OG1 THR C 446 " pdb=" OD1 ASN C 448 " model vdw 1.968 2.440 nonbonded pdb=" O LYS A 706 " pdb=" OG SER A 708 " model vdw 2.049 2.440 nonbonded pdb=" O LYS C 706 " pdb=" OG SER C 708 " model vdw 2.049 2.440 nonbonded pdb=" N ASP C 753 " pdb=" OD1 ASP C 753 " model vdw 2.050 2.520 ... (remaining 177468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 14984 2.51 5 N 3828 2.21 5 O 4428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.000 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.200 Process input model: 59.640 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 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 : 0.015 0.120 23858 Z= 0.997 Angle : 1.223 13.288 32586 Z= 0.662 Chirality : 0.070 1.607 3914 Planarity : 0.006 0.053 4132 Dihedral : 15.422 107.474 8086 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.83 % Allowed : 21.19 % Favored : 77.98 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -5.90 (0.11), residues: 3138 helix: -3.34 (0.11), residues: 1132 sheet: -4.08 (0.19), residues: 370 loop : -4.43 (0.12), residues: 1636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 47 residues processed: 262 average time/residue: 0.2690 time to fit residues: 120.9978 Evaluate side-chains 220 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 173 time to evaluate : 2.725 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.1914 time to fit residues: 20.9841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 160 optimal weight: 40.0000 chunk 127 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 GLN A 577 GLN A 740 GLN ** A 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 486 HIS C 577 GLN ** C 748 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 486 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 23858 Z= 0.412 Angle : 0.809 9.472 32586 Z= 0.429 Chirality : 0.050 0.532 3914 Planarity : 0.005 0.101 4132 Dihedral : 9.609 108.442 3408 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.46 % Favored : 87.35 % Rotamer Outliers : 4.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.42 (0.13), residues: 3138 helix: -1.76 (0.13), residues: 1180 sheet: -3.43 (0.21), residues: 372 loop : -3.85 (0.13), residues: 1586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 208 time to evaluate : 3.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 60 residues processed: 302 average time/residue: 0.2806 time to fit residues: 144.3527 Evaluate side-chains 243 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 183 time to evaluate : 2.723 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.2022 time to fit residues: 26.8716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 237 optimal weight: 30.0000 chunk 194 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 308 optimal weight: 0.2980 chunk 254 optimal weight: 0.0970 chunk 283 optimal weight: 0.5980 chunk 97 optimal weight: 30.0000 chunk 229 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 HIS A 801 HIS B 152 GLN C 278 ASN C 384 GLN C 748 HIS D 152 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 23858 Z= 0.191 Angle : 0.658 11.106 32586 Z= 0.349 Chirality : 0.046 0.458 3914 Planarity : 0.005 0.105 4132 Dihedral : 8.903 105.826 3408 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.69 % Favored : 90.12 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.14), residues: 3138 helix: -0.36 (0.15), residues: 1184 sheet: -2.94 (0.23), residues: 350 loop : -3.31 (0.14), residues: 1604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 29 residues processed: 278 average time/residue: 0.2840 time to fit residues: 135.7704 Evaluate side-chains 226 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2260 time to fit residues: 15.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 191 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 chunk 271 optimal weight: 6.9990 chunk 81 optimal weight: 50.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 278 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN C 731 ASN C 801 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23858 Z= 0.206 Angle : 0.653 10.571 32586 Z= 0.342 Chirality : 0.046 0.457 3914 Planarity : 0.004 0.074 4132 Dihedral : 8.662 104.180 3408 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.82 % Favored : 89.99 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.14), residues: 3138 helix: 0.10 (0.15), residues: 1188 sheet: -2.68 (0.23), residues: 380 loop : -3.20 (0.14), residues: 1570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 205 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 34 residues processed: 249 average time/residue: 0.2796 time to fit residues: 121.4068 Evaluate side-chains 226 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1952 time to fit residues: 16.3078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 209 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 23858 Z= 0.230 Angle : 0.641 7.044 32586 Z= 0.336 Chirality : 0.045 0.452 3914 Planarity : 0.004 0.091 4132 Dihedral : 8.571 104.374 3408 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.46 % Favored : 90.34 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.15), residues: 3138 helix: 0.36 (0.15), residues: 1180 sheet: -2.54 (0.24), residues: 376 loop : -3.04 (0.14), residues: 1582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 195 time to evaluate : 2.976 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 228 average time/residue: 0.2797 time to fit residues: 110.7424 Evaluate side-chains 212 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 2.767 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2117 time to fit residues: 13.1045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.4980 chunk 273 optimal weight: 0.2980 chunk 59 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 252 optimal weight: 20.0000 chunk 140 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN A 731 ASN C 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 23858 Z= 0.167 Angle : 0.617 12.460 32586 Z= 0.320 Chirality : 0.044 0.428 3914 Planarity : 0.004 0.096 4132 Dihedral : 8.349 103.828 3408 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.16 % Favored : 91.65 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 3138 helix: 0.63 (0.15), residues: 1182 sheet: -2.35 (0.24), residues: 372 loop : -2.88 (0.15), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 2.809 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 231 average time/residue: 0.2853 time to fit residues: 112.6898 Evaluate side-chains 205 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 192 time to evaluate : 2.738 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2203 time to fit residues: 9.3355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 chunk 169 optimal weight: 0.0040 chunk 302 optimal weight: 1.9990 chunk 189 optimal weight: 10.0000 chunk 184 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 23858 Z= 0.321 Angle : 0.687 10.170 32586 Z= 0.359 Chirality : 0.046 0.451 3914 Planarity : 0.005 0.088 4132 Dihedral : 8.513 104.998 3408 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.42 % Favored : 89.39 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 3138 helix: 0.62 (0.15), residues: 1170 sheet: -2.40 (0.24), residues: 388 loop : -2.86 (0.15), residues: 1580 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 2.740 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 223 average time/residue: 0.2818 time to fit residues: 109.4792 Evaluate side-chains 205 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 2.484 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2144 time to fit residues: 11.5794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 206 optimal weight: 0.4980 chunk 149 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 overall best weight: 3.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 23858 Z= 0.275 Angle : 0.668 13.382 32586 Z= 0.348 Chirality : 0.046 0.445 3914 Planarity : 0.005 0.108 4132 Dihedral : 8.501 104.645 3408 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.31 % Favored : 90.50 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.15), residues: 3138 helix: 0.67 (0.15), residues: 1180 sheet: -2.39 (0.23), residues: 388 loop : -2.83 (0.15), residues: 1570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 2.722 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 16 residues processed: 208 average time/residue: 0.2866 time to fit residues: 103.3149 Evaluate side-chains 203 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2250 time to fit residues: 10.3244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 chunk 282 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 86 optimal weight: 0.0030 chunk 254 optimal weight: 0.0370 chunk 266 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 overall best weight: 1.3472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 23858 Z= 0.178 Angle : 0.633 10.727 32586 Z= 0.327 Chirality : 0.045 0.417 3914 Planarity : 0.005 0.111 4132 Dihedral : 8.300 104.032 3408 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.73 % Favored : 91.08 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.15), residues: 3138 helix: 0.85 (0.16), residues: 1180 sheet: -2.23 (0.25), residues: 370 loop : -2.71 (0.15), residues: 1588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 2.738 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 207 average time/residue: 0.2832 time to fit residues: 101.3896 Evaluate side-chains 196 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 187 time to evaluate : 2.688 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2172 time to fit residues: 7.1192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 312 optimal weight: 0.9990 chunk 287 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 192 optimal weight: 1.9990 chunk 152 optimal weight: 0.0270 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 23858 Z= 0.175 Angle : 0.629 10.866 32586 Z= 0.322 Chirality : 0.045 0.404 3914 Planarity : 0.005 0.111 4132 Dihedral : 8.149 104.041 3408 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.03 % Favored : 91.84 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.64 (0.15), residues: 3138 helix: 0.96 (0.16), residues: 1178 sheet: -2.11 (0.24), residues: 392 loop : -2.54 (0.15), residues: 1568 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 198 time to evaluate : 2.818 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 202 average time/residue: 0.2960 time to fit residues: 103.7836 Evaluate side-chains 199 residues out of total 2750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 192 time to evaluate : 2.759 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2265 time to fit residues: 6.5319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 10.0000 chunk 265 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 229 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 45 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 HIS D 672 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.088289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066411 restraints weight = 92920.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066135 restraints weight = 60776.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.066756 restraints weight = 49293.873| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 23858 Z= 0.242 Angle : 0.662 10.147 32586 Z= 0.338 Chirality : 0.045 0.414 3914 Planarity : 0.004 0.084 4132 Dihedral : 8.240 104.537 3408 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.86 % Favored : 90.95 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.64 (0.15), residues: 3138 helix: 0.94 (0.16), residues: 1182 sheet: -2.12 (0.25), residues: 368 loop : -2.52 (0.15), residues: 1588 =============================================================================== Job complete usr+sys time: 3504.36 seconds wall clock time: 65 minutes 27.86 seconds (3927.86 seconds total)