Starting phenix.real_space_refine on Mon Sep 14 08:48:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wi0_21681/09_2026/6wi0_21681.map" } resolution = 4.27 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 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= 0.014 sd= 0.788 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9484 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 106 5.16 5 Cl 4 4.86 5 C 14200 2.51 5 N 3586 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21964 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 5545 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 32, 'TRANS': 759} Chain breaks: 4 Unresolved non-hydrogen bonds: 732 Unresolved non-hydrogen angles: 880 Unresolved non-hydrogen dihedrals: 616 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 25, 'TRP:plan': 1, 'GLN:plan1': 12, 'GLU:plan': 38, 'HIS:plan': 9, 'PHE:plan': 2, 'ASP:plan': 18, 'ASN:plan1': 11, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 484 Chain: "B" Number of atoms: 5356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5356 Classifications: {'peptide': 764} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 26, 'TRANS': 737} Chain breaks: 4 Unresolved non-hydrogen bonds: 715 Unresolved non-hydrogen angles: 868 Unresolved non-hydrogen dihedrals: 619 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 20, 'GLU:plan': 30, 'HIS:plan': 7, 'PHE:plan': 8, 'ARG:plan': 18, 'GLN:plan1': 11, 'TYR:plan': 9, 'ASN:plan1': 7} Unresolved non-hydrogen planarities: 479 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: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Classifications: {'peptide': 1} Chain: "B" 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 Restraints were copied for chains: C, D, F Time building chain proxies: 10.18, per 1000 atoms: 0.46 Number of scatterers: 21964 At special positions: 0 Unit cell: (138.37, 154.81, 183.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 106 16.00 O 4068 8.00 N 3586 7.00 C 14200 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS D 557 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.01 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 475 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.04 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " 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=2, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 542 " " NAG D 901 " - " ASN D 542 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 958.1 milliseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB QGM A1001 " pdb=" CB QGM C1001 " Number of C-beta restraints generated: 5816 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 30 sheets defined 42.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 36 through 53 removed outlier: 3.534A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.704A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.692A pdb=" N GLY A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.614A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 150 through 158 removed outlier: 3.573A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.959A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.651A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 4.074A pdb=" N VAL A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 277 through 283 removed outlier: 4.087A pdb=" N ARG A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.506A pdb=" N GLN A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.180A pdb=" N SER A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 489 removed outlier: 3.988A pdb=" N ARG A 489 " --> pdb=" O ILE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 removed outlier: 3.507A pdb=" N GLY A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 548 removed outlier: 3.648A pdb=" N ILE A 548 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 604 removed outlier: 3.840A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.757A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 678 removed outlier: 4.453A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 709 through 717 removed outlier: 4.098A pdb=" N TYR A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 734 through 744 removed outlier: 4.328A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 761 removed outlier: 4.533A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 804 removed outlier: 3.514A pdb=" N VAL A 793 " --> pdb=" O TRP A 789 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU A 795 " --> pdb=" O GLN A 791 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 796 " --> pdb=" O GLN A 792 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 804 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 812 Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'A' and resid 835 through 861 removed outlier: 3.635A pdb=" N MET A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.147A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 340 removed outlier: 3.890A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.574A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 517 through 523 removed outlier: 3.679A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 523 " --> pdb=" O ARG B 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 517 through 523' Processing helix chain 'B' and resid 555 through 575 removed outlier: 4.236A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA B 571 " --> pdb=" O LEU B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.930A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 654 removed outlier: 3.605A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 707 removed outlier: 7.144A pdb=" N GLU B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) 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 removed outlier: 3.731A pdb=" N LEU B 718 " --> pdb=" O VAL B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 4.784A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 785 removed outlier: 4.348A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.660A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 842 removed outlier: 4.013A pdb=" N TYR B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'C' and resid 36 through 53 removed outlier: 3.535A pdb=" N GLN C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 3.704A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.692A pdb=" N GLY C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.614A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 Processing helix chain 'C' and resid 150 through 158 removed outlier: 3.573A pdb=" N MET C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 removed outlier: 3.958A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 235 removed outlier: 3.651A pdb=" N GLU C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 removed outlier: 4.074A pdb=" N VAL C 252 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 257 " --> pdb=" O TYR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 277 through 283 removed outlier: 4.087A pdb=" N ARG C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 315 removed outlier: 3.506A pdb=" N GLN C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 removed outlier: 4.179A pdb=" N SER C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 489 removed outlier: 3.989A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 529 removed outlier: 3.508A pdb=" N GLY C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 548 removed outlier: 3.648A pdb=" N ILE C 548 " --> pdb=" O ALA C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 604 removed outlier: 3.839A pdb=" N HIS C 592 " --> pdb=" O GLY C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.757A pdb=" N LEU C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 678 removed outlier: 4.452A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 663 " --> pdb=" O GLY C 659 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 709 through 717 removed outlier: 4.097A pdb=" N TYR C 713 " --> pdb=" O SER C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 728 Processing helix chain 'C' and resid 734 through 744 removed outlier: 4.329A pdb=" N ILE C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN C 740 " --> pdb=" O ALA C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 761 removed outlier: 4.533A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 804 removed outlier: 3.513A pdb=" N VAL C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU C 795 " --> pdb=" O GLN C 791 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 803 " --> pdb=" O LYS C 799 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C 804 " --> pdb=" O SER C 800 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 812 Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'C' and resid 835 through 861 removed outlier: 3.635A pdb=" N MET C 839 " --> pdb=" O ALA C 835 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE C 853 " --> pdb=" O ILE C 849 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ILE C 854 " --> pdb=" O PHE C 850 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 856 " --> pdb=" O ILE C 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 214 through 221 Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.147A pdb=" N THR D 238 " --> pdb=" O LYS D 234 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.890A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.573A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 517 through 523 removed outlier: 3.679A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL D 522 " --> pdb=" O GLU D 518 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 523 " --> pdb=" O ARG D 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 517 through 523' Processing helix chain 'D' and resid 555 through 575 removed outlier: 4.235A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.931A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 654 removed outlier: 3.605A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 653 " --> pdb=" O ASN D 649 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 707 removed outlier: 7.143A pdb=" N GLU D 701 " --> pdb=" O ASN D 697 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET D 702 " --> pdb=" O ASN D 698 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N TYR D 705 " --> pdb=" O GLU D 701 " (cutoff:3.500A) 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 removed outlier: 3.731A pdb=" N LEU D 718 " --> pdb=" O VAL D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.784A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 785 removed outlier: 4.350A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.659A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 842 removed outlier: 4.012A pdb=" N TYR D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 843 through 845 No H-bonds generated for 'chain 'D' and resid 843 through 845' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 65 Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 216 removed outlier: 7.717A pdb=" N ILE A 163 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 215 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 165 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 292 removed outlier: 5.998A pdb=" N TYR A 372 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE A 387 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 374 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 6.475A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL A 422 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 431 through 433 Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 511 removed outlier: 3.651A pdb=" N VAL A 511 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AA8, first strand: chain 'A' and resid 749 through 753 Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.038A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 124 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 198 through 204 removed outlier: 7.739A pdb=" N PHE B 169 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 202 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 171 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU B 204 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 173 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS B 372 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.599A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 524 through 525 removed outlier: 3.684A pdb=" N ILE B 766 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.078A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 729 through 732 Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 65 Processing sheet with id=AB8, first strand: chain 'C' and resid 211 through 216 removed outlier: 7.718A pdb=" N ILE C 163 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 215 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU C 165 " --> pdb=" O VAL C 215 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 288 through 292 removed outlier: 5.998A pdb=" N TYR C 372 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 387 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 374 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 497 through 498 removed outlier: 6.475A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL C 535 " --> pdb=" O VAL C 422 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA C 536 " --> pdb=" O GLY C 780 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY C 780 " --> pdb=" O ALA C 536 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 431 through 433 Processing sheet with id=AC3, first strand: chain 'C' and resid 510 through 511 removed outlier: 3.651A pdb=" N VAL C 511 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 753 Processing sheet with id=AC6, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.038A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 124 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 204 removed outlier: 7.739A pdb=" N PHE D 169 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL D 202 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 171 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LEU D 204 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 173 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 343 through 344 Processing sheet with id=AC9, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.600A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 524 through 525 removed outlier: 3.683A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 530 through 532 removed outlier: 4.077A pdb=" N ILE D 530 " --> pdb=" O TYR D 762 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 729 through 732 926 hydrogen bonds defined for protein. 2598 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: 4.44 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3564 1.31 - 1.44: 6012 1.44 - 1.57: 12684 1.57 - 1.70: 0 1.70 - 1.82: 174 Bond restraints: 22434 Sorted by residual: bond pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 1.347 1.473 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 1.347 1.473 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" ND2 QGM C1001 " pdb=" CAR QGM C1001 " ideal model delta sigma weight residual 1.354 1.448 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" ND2 QGM A1001 " pdb=" CAR QGM A1001 " ideal model delta sigma weight residual 1.354 1.448 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAR QGM A1001 " pdb=" NAN QGM A1001 " ideal model delta sigma weight residual 1.376 1.454 -0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 22429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 30535 2.98 - 5.97: 234 5.97 - 8.95: 27 8.95 - 11.94: 2 11.94 - 14.92: 2 Bond angle restraints: 30800 Sorted by residual: angle pdb=" N VAL D 576 " pdb=" CA VAL D 576 " pdb=" C VAL D 576 " ideal model delta sigma weight residual 113.39 105.61 7.78 1.47e+00 4.63e-01 2.80e+01 angle pdb=" N VAL B 576 " pdb=" CA VAL B 576 " pdb=" C VAL B 576 " ideal model delta sigma weight residual 113.39 105.61 7.78 1.47e+00 4.63e-01 2.80e+01 angle pdb=" CA QGM A1001 " pdb=" N QGM A1001 " pdb=" CAV QGM A1001 " ideal model delta sigma weight residual 123.80 108.88 14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" CA QGM C1001 " pdb=" N QGM C1001 " pdb=" CAV QGM C1001 " ideal model delta sigma weight residual 123.80 108.88 14.92 3.00e+00 1.11e-01 2.47e+01 angle pdb=" C ILE B 85 " pdb=" N CYS B 86 " pdb=" CA CYS B 86 " ideal model delta sigma weight residual 121.14 114.38 6.76 1.75e+00 3.27e-01 1.49e+01 ... (remaining 30795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 11807 17.32 - 34.63: 885 34.63 - 51.95: 192 51.95 - 69.27: 38 69.27 - 86.58: 10 Dihedral angle restraints: 12932 sinusoidal: 3932 harmonic: 9000 Sorted by residual: dihedral pdb=" CB CYS A 831 " pdb=" SG CYS A 831 " pdb=" SG CYS D 557 " pdb=" CB CYS D 557 " ideal model delta sinusoidal sigma weight residual 93.00 6.42 86.58 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS B 557 " pdb=" SG CYS B 557 " pdb=" SG CYS C 831 " pdb=" CB CYS C 831 " ideal model delta sinusoidal sigma weight residual 93.00 6.79 86.21 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CA GLU D 412 " pdb=" C GLU D 412 " pdb=" N GLU D 413 " pdb=" CA GLU D 413 " ideal model delta harmonic sigma weight residual 180.00 135.06 44.94 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.307: 3806 0.307 - 0.613: 2 0.613 - 0.920: 0 0.920 - 1.227: 0 1.227 - 1.533: 2 Chirality restraints: 3810 Sorted by residual: 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 -0.87 -1.53 2.00e-02 2.50e+03 5.88e+03 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 -0.87 -1.53 2.00e-02 2.50e+03 5.87e+03 chirality pdb=" CG QGM A1001 " pdb=" CB QGM A1001 " pdb=" CD1 QGM A1001 " pdb=" ND2 QGM A1001 " both_signs ideal model delta sigma weight residual False -2.43 -2.85 0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 3807 not shown) Planarity restraints: 3886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 103 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO C 104 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 103 " -0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO A 104 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 104 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 104 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 258 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 259 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 259 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 259 " -0.026 5.00e-02 4.00e+02 ... (remaining 3883 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 770 2.69 - 3.24: 24547 3.24 - 3.79: 33931 3.79 - 4.35: 41571 4.35 - 4.90: 63324 Nonbonded interactions: 164143 Sorted by model distance: nonbonded pdb=" O MET B 829 " pdb=" OG SER B 832 " model vdw 2.134 3.040 nonbonded pdb=" O MET D 829 " pdb=" OG SER D 832 " model vdw 2.134 3.040 nonbonded pdb=" OG SER C 93 " pdb=" OG1 THR C 122 " model vdw 2.151 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OG1 THR A 122 " model vdw 2.152 3.040 nonbonded pdb=" OG SER C 762 " pdb=" O TYR C 816 " model vdw 2.167 3.040 ... (remaining 164138 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: 0.05 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.830 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 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 : 0.005 0.126 22460 Z= 0.265 Angle : 0.876 36.446 30854 Z= 0.457 Chirality : 0.058 1.533 3810 Planarity : 0.004 0.054 3882 Dihedral : 13.415 83.913 7062 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.19 % Favored : 89.62 % Rotamer: Outliers : 0.60 % Allowed : 7.54 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.12), residues: 3072 helix: -2.57 (0.12), residues: 1112 sheet: -3.00 (0.23), residues: 350 loop : -3.43 (0.13), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 124 TYR 0.013 0.002 TYR A 713 PHE 0.012 0.002 PHE B 784 TRP 0.014 0.002 TRP B 796 HIS 0.005 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.26 (22434) covalent geometry : angle 0.77365 / 0.44 (30800) SS BOND : bond 0.00887 / 0.80 ( 18) SS BOND : angle 1.97253 / 1.38 ( 36) hydrogen bonds : bond 0.17544 / 12.04 ( 926) hydrogen bonds : angle 7.18338 / 5.23 ( 2598) Misc. bond : bond 0.00059 / 0.03 ( 2) link_BETA1-4 : bond 0.06533 / 3.28 ( 2) link_BETA1-4 : angle 25.19395 / 14.68 ( 6) link_NAG-ASN : bond 0.01353 / 0.69 ( 4) link_NAG-ASN : angle 10.43264 / 6.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 259 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.6010 (mtp) cc_final: 0.5590 (mtm) REVERT: B 176 PHE cc_start: 0.6067 (t80) cc_final: 0.5649 (t80) REVERT: B 515 ILE cc_start: 0.8929 (mt) cc_final: 0.8690 (tt) REVERT: C 154 MET cc_start: 0.6230 (mtp) cc_final: 0.5757 (mtm) REVERT: D 300 ILE cc_start: 0.6747 (tt) cc_final: 0.6540 (mt) outliers start: 12 outliers final: 4 residues processed: 267 average time/residue: 0.1284 time to fit residues: 58.2315 Evaluate side-chains 190 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.0270 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.7980 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN A 147 GLN A 414 GLN A 425 HIS A 426 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 HIS B 153 GLN B 192 ASN B 341 ASN B 359 HIS B 817 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN C 147 GLN C 414 GLN C 425 HIS C 426 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 192 ASN D 359 HIS D 817 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.070844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.056855 restraints weight = 133006.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.058206 restraints weight = 86658.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059820 restraints weight = 56503.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.059906 restraints weight = 42621.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059999 restraints weight = 39342.340| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22460 Z= 0.151 Angle : 0.679 17.246 30854 Z= 0.340 Chirality : 0.045 0.196 3810 Planarity : 0.004 0.061 3882 Dihedral : 5.884 56.031 3232 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.79 % Favored : 91.08 % Rotamer: Outliers : 0.10 % Allowed : 6.19 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.14), residues: 3072 helix: -0.88 (0.14), residues: 1166 sheet: -2.60 (0.22), residues: 402 loop : -2.86 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 124 TYR 0.015 0.002 TYR B 287 PHE 0.013 0.001 PHE B 681 TRP 0.021 0.001 TRP B 796 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (22434) covalent geometry : angle 0.65118 / 0.33 (30800) SS BOND : bond 0.00539 / 0.42 ( 18) SS BOND : angle 1.78513 / 1.25 ( 36) hydrogen bonds : bond 0.04753 / 3.30 ( 926) hydrogen bonds : angle 5.37278 / 3.92 ( 2598) Misc. bond : bond 0.00228 / 0.11 ( 2) link_BETA1-4 : bond 0.01824 / 0.90 ( 2) link_BETA1-4 : angle 3.90615 / 2.16 ( 6) link_NAG-ASN : bond 0.01470 / 0.75 ( 4) link_NAG-ASN : angle 8.85862 / 5.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 240 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8789 (mmm) cc_final: 0.8172 (mmm) REVERT: A 261 MET cc_start: 0.8212 (mmm) cc_final: 0.7949 (mmp) REVERT: A 523 MET cc_start: 0.8511 (tpp) cc_final: 0.7887 (tpp) REVERT: A 628 MET cc_start: 0.8508 (tmm) cc_final: 0.8090 (tmm) REVERT: A 723 MET cc_start: 0.8060 (mmm) cc_final: 0.7736 (mmm) REVERT: B 132 MET cc_start: 0.8983 (mmp) cc_final: 0.8250 (mmm) REVERT: B 133 ILE cc_start: 0.8560 (pt) cc_final: 0.8213 (pt) REVERT: B 134 MET cc_start: 0.8781 (pmm) cc_final: 0.8344 (pmm) REVERT: B 157 MET cc_start: 0.9383 (mmm) cc_final: 0.9027 (tmm) REVERT: B 321 CYS cc_start: 0.1975 (p) cc_final: 0.1575 (p) REVERT: B 503 MET cc_start: 0.8672 (mpp) cc_final: 0.8319 (mpp) REVERT: B 698 ASN cc_start: 0.8119 (t0) cc_final: 0.7747 (t0) REVERT: C 261 MET cc_start: 0.8252 (mmm) cc_final: 0.7984 (mmp) REVERT: D 132 MET cc_start: 0.9133 (mmp) cc_final: 0.8247 (mmm) REVERT: D 136 ASP cc_start: 0.8503 (t70) cc_final: 0.8198 (t0) REVERT: D 166 TRP cc_start: 0.8366 (m100) cc_final: 0.8026 (m100) REVERT: D 321 CYS cc_start: 0.1361 (p) cc_final: 0.1065 (p) REVERT: D 457 CYS cc_start: 0.7611 (m) cc_final: 0.7380 (m) REVERT: D 503 MET cc_start: 0.8768 (ptp) cc_final: 0.8257 (ptt) REVERT: D 698 ASN cc_start: 0.8533 (t0) cc_final: 0.8082 (t0) outliers start: 2 outliers final: 2 residues processed: 242 average time/residue: 0.1211 time to fit residues: 50.7810 Evaluate side-chains 194 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 59 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.071722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058057 restraints weight = 133102.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059202 restraints weight = 83806.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060421 restraints weight = 55417.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060574 restraints weight = 46085.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060607 restraints weight = 41066.347| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22460 Z= 0.140 Angle : 0.633 16.184 30854 Z= 0.317 Chirality : 0.044 0.162 3810 Planarity : 0.004 0.067 3882 Dihedral : 5.523 56.163 3232 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.11 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.15), residues: 3072 helix: -0.04 (0.15), residues: 1166 sheet: -2.47 (0.22), residues: 428 loop : -2.40 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 187 TYR 0.013 0.001 TYR D 287 PHE 0.041 0.002 PHE B 241 TRP 0.021 0.001 TRP D 796 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (22434) covalent geometry : angle 0.60668 / 0.31 (30800) SS BOND : bond 0.00871 / 0.49 ( 18) SS BOND : angle 1.75917 / 1.23 ( 36) hydrogen bonds : bond 0.04024 / 2.83 ( 926) hydrogen bonds : angle 4.96742 / 3.63 ( 2598) Misc. bond : bond 0.00226 / 0.11 ( 2) link_BETA1-4 : bond 0.00592 / 0.30 ( 2) link_BETA1-4 : angle 2.84119 / 1.56 ( 6) link_NAG-ASN : bond 0.01335 / 0.68 ( 4) link_NAG-ASN : angle 8.42304 / 5.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8864 (mmm) cc_final: 0.8205 (mmm) REVERT: A 261 MET cc_start: 0.8357 (mmm) cc_final: 0.7540 (mmt) REVERT: A 493 PHE cc_start: 0.8529 (m-80) cc_final: 0.8061 (m-80) REVERT: A 628 MET cc_start: 0.8457 (tmm) cc_final: 0.8119 (tmm) REVERT: B 132 MET cc_start: 0.9124 (mmp) cc_final: 0.8326 (mmm) REVERT: B 133 ILE cc_start: 0.8840 (pt) cc_final: 0.8338 (pt) REVERT: B 134 MET cc_start: 0.9039 (pmm) cc_final: 0.8437 (pmm) REVERT: B 136 ASP cc_start: 0.8528 (t70) cc_final: 0.8231 (t0) REVERT: B 142 MET cc_start: 0.8171 (mmt) cc_final: 0.7963 (mmt) REVERT: B 321 CYS cc_start: 0.1639 (p) cc_final: 0.1237 (p) REVERT: B 503 MET cc_start: 0.8547 (mpp) cc_final: 0.8169 (mpp) REVERT: B 646 TYR cc_start: 0.9127 (t80) cc_final: 0.8790 (t80) REVERT: B 698 ASN cc_start: 0.8001 (t0) cc_final: 0.7580 (t0) REVERT: C 261 MET cc_start: 0.8359 (mmm) cc_final: 0.8025 (mmt) REVERT: C 723 MET cc_start: 0.7381 (mmp) cc_final: 0.6831 (mmt) REVERT: D 132 MET cc_start: 0.9211 (mmp) cc_final: 0.8472 (mmm) REVERT: D 133 ILE cc_start: 0.8646 (pt) cc_final: 0.8445 (pt) REVERT: D 136 ASP cc_start: 0.8568 (t70) cc_final: 0.8283 (t0) REVERT: D 142 MET cc_start: 0.8057 (mmt) cc_final: 0.7664 (mmm) REVERT: D 321 CYS cc_start: 0.1116 (p) cc_final: 0.0855 (p) REVERT: D 503 MET cc_start: 0.8850 (ptp) cc_final: 0.8636 (ptp) REVERT: D 646 TYR cc_start: 0.9130 (t80) cc_final: 0.8763 (t80) REVERT: D 698 ASN cc_start: 0.8454 (t0) cc_final: 0.8061 (t0) REVERT: D 706 MET cc_start: 0.9196 (mmm) cc_final: 0.8865 (mmm) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1224 time to fit residues: 52.9544 Evaluate side-chains 188 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 234 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 181 optimal weight: 0.0470 chunk 201 optimal weight: 0.0020 chunk 214 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.073417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059114 restraints weight = 126297.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060984 restraints weight = 75962.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.061756 restraints weight = 47265.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.062217 restraints weight = 41823.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062323 restraints weight = 38507.879| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22460 Z= 0.104 Angle : 0.589 14.977 30854 Z= 0.291 Chirality : 0.043 0.177 3810 Planarity : 0.004 0.065 3882 Dihedral : 5.108 56.440 3232 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.51 % Favored : 93.36 % Rotamer: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 3072 helix: 0.41 (0.15), residues: 1170 sheet: -1.81 (0.23), residues: 432 loop : -2.09 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 36 TYR 0.016 0.001 TYR D 287 PHE 0.031 0.001 PHE D 842 TRP 0.036 0.001 TRP B 607 HIS 0.002 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (22434) covalent geometry : angle 0.56704 / 0.29 (30800) SS BOND : bond 0.00377 / 0.30 ( 18) SS BOND : angle 1.59169 / 1.06 ( 36) hydrogen bonds : bond 0.03392 / 2.41 ( 926) hydrogen bonds : angle 4.53532 / 3.31 ( 2598) Misc. bond : bond 0.00280 / 0.14 ( 2) link_BETA1-4 : bond 0.00286 / 0.15 ( 2) link_BETA1-4 : angle 2.30045 / 1.24 ( 6) link_NAG-ASN : bond 0.01325 / 0.68 ( 4) link_NAG-ASN : angle 7.57967 / 4.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8876 (mmm) cc_final: 0.8239 (mmm) REVERT: A 261 MET cc_start: 0.8386 (mmm) cc_final: 0.7728 (mmt) REVERT: A 493 PHE cc_start: 0.8513 (m-80) cc_final: 0.8061 (m-80) REVERT: A 628 MET cc_start: 0.8440 (tmm) cc_final: 0.7989 (tmm) REVERT: A 719 GLU cc_start: 0.7690 (tp30) cc_final: 0.7335 (tm-30) REVERT: B 132 MET cc_start: 0.9057 (mmp) cc_final: 0.8242 (mmm) REVERT: B 134 MET cc_start: 0.9114 (pmm) cc_final: 0.8483 (pmm) REVERT: B 321 CYS cc_start: 0.0969 (p) cc_final: 0.0716 (p) REVERT: B 646 TYR cc_start: 0.9065 (t80) cc_final: 0.8732 (t80) REVERT: B 698 ASN cc_start: 0.7892 (t0) cc_final: 0.7474 (t0) REVERT: C 261 MET cc_start: 0.8423 (mmm) cc_final: 0.8194 (mmt) REVERT: C 628 MET cc_start: 0.8226 (tmm) cc_final: 0.7704 (tmm) REVERT: C 723 MET cc_start: 0.7610 (mmp) cc_final: 0.7195 (mmt) REVERT: D 132 MET cc_start: 0.9087 (mmp) cc_final: 0.8584 (mmm) REVERT: D 133 ILE cc_start: 0.8674 (pt) cc_final: 0.8450 (pt) REVERT: D 136 ASP cc_start: 0.8548 (t70) cc_final: 0.8245 (t0) REVERT: D 142 MET cc_start: 0.7767 (mmt) cc_final: 0.7370 (mmm) REVERT: D 321 CYS cc_start: 0.0800 (p) cc_final: 0.0536 (p) REVERT: D 646 TYR cc_start: 0.9104 (t80) cc_final: 0.8692 (t80) REVERT: D 698 ASN cc_start: 0.8377 (t0) cc_final: 0.7980 (t0) REVERT: D 706 MET cc_start: 0.9054 (mmm) cc_final: 0.8797 (mmt) outliers start: 2 outliers final: 0 residues processed: 272 average time/residue: 0.1257 time to fit residues: 58.4578 Evaluate side-chains 207 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 60 optimal weight: 9.9990 chunk 250 optimal weight: 30.0000 chunk 193 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 198 optimal weight: 0.1980 chunk 106 optimal weight: 50.0000 chunk 162 optimal weight: 20.0000 chunk 276 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.070215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055749 restraints weight = 129954.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057250 restraints weight = 78189.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058276 restraints weight = 55822.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.058958 restraints weight = 44395.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.059422 restraints weight = 38012.401| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22460 Z= 0.207 Angle : 0.676 14.327 30854 Z= 0.342 Chirality : 0.045 0.179 3810 Planarity : 0.004 0.064 3882 Dihedral : 5.403 54.570 3232 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.18 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.15), residues: 3072 helix: 0.26 (0.15), residues: 1174 sheet: -2.09 (0.23), residues: 444 loop : -2.04 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 36 TYR 0.029 0.002 TYR D 167 PHE 0.024 0.002 PHE B 241 TRP 0.037 0.002 TRP B 610 HIS 0.006 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (22434) covalent geometry : angle 0.65686 / 0.34 (30800) SS BOND : bond 0.00467 / 0.32 ( 18) SS BOND : angle 1.63786 / 1.12 ( 36) hydrogen bonds : bond 0.03928 / 2.75 ( 926) hydrogen bonds : angle 4.86856 / 3.54 ( 2598) Misc. bond : bond 0.00125 / 0.06 ( 2) link_BETA1-4 : bond 0.00902 / 0.45 ( 2) link_BETA1-4 : angle 2.25769 / 1.21 ( 6) link_NAG-ASN : bond 0.01116 / 0.57 ( 4) link_NAG-ASN : angle 7.56795 / 4.69 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8534 (t0) cc_final: 0.8268 (t0) REVERT: A 261 MET cc_start: 0.8629 (mmm) cc_final: 0.8403 (mmp) REVERT: A 493 PHE cc_start: 0.8470 (m-80) cc_final: 0.7988 (m-80) REVERT: A 628 MET cc_start: 0.8463 (tmm) cc_final: 0.8051 (tmm) REVERT: B 132 MET cc_start: 0.9092 (mmp) cc_final: 0.8279 (mmm) REVERT: B 134 MET cc_start: 0.9153 (pmm) cc_final: 0.8407 (pmm) REVERT: B 321 CYS cc_start: 0.1187 (p) cc_final: 0.0854 (p) REVERT: B 646 TYR cc_start: 0.9103 (t80) cc_final: 0.8796 (t80) REVERT: C 130 ASP cc_start: 0.8310 (t0) cc_final: 0.8076 (t0) REVERT: C 493 PHE cc_start: 0.8537 (m-80) cc_final: 0.8070 (m-80) REVERT: C 628 MET cc_start: 0.8356 (tmm) cc_final: 0.7819 (tmm) REVERT: D 132 MET cc_start: 0.9211 (mmp) cc_final: 0.8590 (mmm) REVERT: D 136 ASP cc_start: 0.8603 (t70) cc_final: 0.8307 (t0) REVERT: D 277 LEU cc_start: 0.8021 (mt) cc_final: 0.7817 (mt) REVERT: D 321 CYS cc_start: 0.1058 (p) cc_final: 0.0634 (p) REVERT: D 698 ASN cc_start: 0.8301 (t0) cc_final: 0.7836 (t0) REVERT: D 706 MET cc_start: 0.9200 (mmm) cc_final: 0.8879 (mmt) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1175 time to fit residues: 49.4450 Evaluate side-chains 192 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 258 optimal weight: 0.0870 chunk 257 optimal weight: 5.9990 chunk 146 optimal weight: 0.0030 chunk 105 optimal weight: 30.0000 chunk 157 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 244 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 300 optimal weight: 0.4980 chunk 273 optimal weight: 9.9990 overall best weight: 1.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.072662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058108 restraints weight = 126904.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059692 restraints weight = 76281.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060771 restraints weight = 54244.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061500 restraints weight = 42878.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061994 restraints weight = 36446.475| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22460 Z= 0.107 Angle : 0.604 13.336 30854 Z= 0.298 Chirality : 0.043 0.171 3810 Planarity : 0.004 0.062 3882 Dihedral : 5.108 57.588 3232 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 3072 helix: 0.60 (0.16), residues: 1162 sheet: -1.56 (0.23), residues: 450 loop : -1.93 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 36 TYR 0.019 0.001 TYR C 266 PHE 0.035 0.001 PHE D 241 TRP 0.024 0.001 TRP B 610 HIS 0.003 0.001 HIS D 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (22434) covalent geometry : angle 0.58647 / 0.29 (30800) SS BOND : bond 0.00384 / 0.29 ( 18) SS BOND : angle 1.65986 / 1.13 ( 36) hydrogen bonds : bond 0.03489 / 2.48 ( 926) hydrogen bonds : angle 4.53808 / 3.30 ( 2598) Misc. bond : bond 0.00232 / 0.12 ( 2) link_BETA1-4 : bond 0.00575 / 0.29 ( 2) link_BETA1-4 : angle 2.04814 / 1.08 ( 6) link_NAG-ASN : bond 0.01118 / 0.57 ( 4) link_NAG-ASN : angle 6.77315 / 4.12 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8468 (t0) cc_final: 0.8228 (t0) REVERT: A 230 MET cc_start: 0.8858 (mmm) cc_final: 0.8174 (mmm) REVERT: A 261 MET cc_start: 0.8605 (mmm) cc_final: 0.8346 (mmt) REVERT: A 493 PHE cc_start: 0.8422 (m-80) cc_final: 0.7961 (m-80) REVERT: A 628 MET cc_start: 0.8419 (tmm) cc_final: 0.8010 (tmm) REVERT: A 719 GLU cc_start: 0.7716 (tp30) cc_final: 0.7388 (tm-30) REVERT: B 73 MET cc_start: 0.8389 (tpt) cc_final: 0.8105 (tpp) REVERT: B 132 MET cc_start: 0.9127 (mmp) cc_final: 0.8361 (mmm) REVERT: B 134 MET cc_start: 0.9134 (pmm) cc_final: 0.8346 (pmm) REVERT: B 136 ASP cc_start: 0.8522 (t70) cc_final: 0.8230 (t0) REVERT: B 161 MET cc_start: 0.7467 (ptp) cc_final: 0.7178 (ptp) REVERT: B 321 CYS cc_start: 0.0995 (p) cc_final: 0.0514 (p) REVERT: B 503 MET cc_start: 0.9007 (ptp) cc_final: 0.8428 (ptt) REVERT: B 646 TYR cc_start: 0.9020 (t80) cc_final: 0.8684 (t80) REVERT: B 698 ASN cc_start: 0.8005 (t0) cc_final: 0.7637 (t0) REVERT: C 153 GLU cc_start: 0.9270 (mp0) cc_final: 0.9029 (mp0) REVERT: C 493 PHE cc_start: 0.8490 (m-80) cc_final: 0.8036 (m-80) REVERT: C 628 MET cc_start: 0.8336 (tmm) cc_final: 0.7761 (tmm) REVERT: D 132 MET cc_start: 0.9047 (mmp) cc_final: 0.8534 (mmm) REVERT: D 136 ASP cc_start: 0.8524 (t70) cc_final: 0.8262 (t0) REVERT: D 142 MET cc_start: 0.7726 (mmt) cc_final: 0.7377 (mmm) REVERT: D 277 LEU cc_start: 0.7975 (mt) cc_final: 0.7732 (mt) REVERT: D 698 ASN cc_start: 0.8178 (t0) cc_final: 0.7706 (t0) REVERT: D 706 MET cc_start: 0.9121 (mmm) cc_final: 0.8823 (mmt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.1250 time to fit residues: 54.8277 Evaluate side-chains 207 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 196 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 chunk 249 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN D 152 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.072713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058089 restraints weight = 127038.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.059609 restraints weight = 78124.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.060618 restraints weight = 56276.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061308 restraints weight = 45050.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061799 restraints weight = 38710.510| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22460 Z= 0.111 Angle : 0.596 12.254 30854 Z= 0.295 Chirality : 0.043 0.151 3810 Planarity : 0.004 0.062 3882 Dihedral : 4.936 54.226 3232 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.29 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 3072 helix: 0.70 (0.16), residues: 1164 sheet: -1.59 (0.23), residues: 458 loop : -1.79 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 36 TYR 0.013 0.001 TYR D 287 PHE 0.029 0.001 PHE B 563 TRP 0.015 0.001 TRP D 166 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (22434) covalent geometry : angle 0.57900 / 0.29 (30800) SS BOND : bond 0.00540 / 0.40 ( 18) SS BOND : angle 1.78908 / 1.20 ( 36) hydrogen bonds : bond 0.03366 / 2.37 ( 926) hydrogen bonds : angle 4.49333 / 3.26 ( 2598) Misc. bond : bond 0.00195 / 0.10 ( 2) link_BETA1-4 : bond 0.00640 / 0.32 ( 2) link_BETA1-4 : angle 1.98843 / 1.06 ( 6) link_NAG-ASN : bond 0.01015 / 0.52 ( 4) link_NAG-ASN : angle 6.33987 / 3.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8861 (mmm) cc_final: 0.8196 (mmm) REVERT: A 493 PHE cc_start: 0.8408 (m-80) cc_final: 0.7965 (m-80) REVERT: A 523 MET cc_start: 0.8463 (mmt) cc_final: 0.7914 (mmt) REVERT: A 526 LEU cc_start: 0.8622 (pp) cc_final: 0.8309 (pp) REVERT: A 628 MET cc_start: 0.8378 (tmm) cc_final: 0.7995 (tmm) REVERT: A 719 GLU cc_start: 0.7705 (tp30) cc_final: 0.7393 (tm-30) REVERT: B 73 MET cc_start: 0.8360 (tpt) cc_final: 0.8092 (tpp) REVERT: B 132 MET cc_start: 0.9143 (mmp) cc_final: 0.8418 (mmm) REVERT: B 134 MET cc_start: 0.8762 (pmm) cc_final: 0.8376 (pmm) REVERT: B 136 ASP cc_start: 0.8477 (t70) cc_final: 0.8215 (t0) REVERT: B 142 MET cc_start: 0.8116 (mmt) cc_final: 0.7741 (mmp) REVERT: B 321 CYS cc_start: 0.0874 (p) cc_final: 0.0383 (p) REVERT: B 503 MET cc_start: 0.9009 (ptp) cc_final: 0.8426 (ptt) REVERT: B 646 TYR cc_start: 0.9011 (t80) cc_final: 0.8699 (t80) REVERT: B 698 ASN cc_start: 0.7868 (t0) cc_final: 0.7519 (t0) REVERT: C 153 GLU cc_start: 0.9257 (mp0) cc_final: 0.9014 (mp0) REVERT: C 493 PHE cc_start: 0.8465 (m-80) cc_final: 0.7981 (m-80) REVERT: C 628 MET cc_start: 0.8332 (tmm) cc_final: 0.7761 (tmm) REVERT: D 132 MET cc_start: 0.9066 (mmp) cc_final: 0.8523 (mmm) REVERT: D 136 ASP cc_start: 0.8458 (t70) cc_final: 0.8234 (t0) REVERT: D 142 MET cc_start: 0.7629 (mmt) cc_final: 0.7363 (mmp) REVERT: D 277 LEU cc_start: 0.8005 (mt) cc_final: 0.7739 (mt) REVERT: D 698 ASN cc_start: 0.8072 (t0) cc_final: 0.7602 (t0) REVERT: D 706 MET cc_start: 0.9082 (mmm) cc_final: 0.8798 (mmt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1232 time to fit residues: 53.8693 Evaluate side-chains 202 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 95 optimal weight: 40.0000 chunk 31 optimal weight: 0.2980 chunk 124 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 109 optimal weight: 30.0000 chunk 296 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 216 optimal weight: 0.1980 chunk 252 optimal weight: 9.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.072013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.057449 restraints weight = 128129.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.058945 restraints weight = 79289.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.059943 restraints weight = 57362.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060636 restraints weight = 46083.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061108 restraints weight = 39516.358| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22460 Z= 0.140 Angle : 0.616 11.640 30854 Z= 0.305 Chirality : 0.043 0.183 3810 Planarity : 0.004 0.061 3882 Dihedral : 4.975 53.924 3232 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.98 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.16), residues: 3072 helix: 0.72 (0.16), residues: 1164 sheet: -1.73 (0.24), residues: 448 loop : -1.71 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 36 TYR 0.013 0.001 TYR D 167 PHE 0.018 0.001 PHE A 550 TRP 0.035 0.001 TRP B 796 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (22434) covalent geometry : angle 0.60036 / 0.30 (30800) SS BOND : bond 0.00379 / 0.26 ( 18) SS BOND : angle 1.82101 / 1.21 ( 36) hydrogen bonds : bond 0.03392 / 2.39 ( 926) hydrogen bonds : angle 4.54726 / 3.31 ( 2598) Misc. bond : bond 0.00153 / 0.08 ( 2) link_BETA1-4 : bond 0.00703 / 0.35 ( 2) link_BETA1-4 : angle 1.96257 / 1.04 ( 6) link_NAG-ASN : bond 0.00925 / 0.48 ( 4) link_NAG-ASN : angle 6.12942 / 3.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8415 (t0) cc_final: 0.8185 (t0) REVERT: A 493 PHE cc_start: 0.8359 (m-80) cc_final: 0.7942 (m-80) REVERT: A 628 MET cc_start: 0.8377 (tmm) cc_final: 0.8011 (tmm) REVERT: B 73 MET cc_start: 0.8347 (tpt) cc_final: 0.8076 (tpp) REVERT: B 132 MET cc_start: 0.9243 (mmp) cc_final: 0.8534 (mmm) REVERT: B 134 MET cc_start: 0.8535 (pmm) cc_final: 0.8052 (pmm) REVERT: B 136 ASP cc_start: 0.8481 (t70) cc_final: 0.8215 (t0) REVERT: B 142 MET cc_start: 0.8117 (mmt) cc_final: 0.7818 (mmt) REVERT: B 503 MET cc_start: 0.9006 (ptp) cc_final: 0.8453 (ptt) REVERT: B 646 TYR cc_start: 0.9045 (t80) cc_final: 0.8733 (t80) REVERT: B 698 ASN cc_start: 0.7905 (t0) cc_final: 0.7567 (t0) REVERT: C 153 GLU cc_start: 0.9244 (mp0) cc_final: 0.9022 (mp0) REVERT: C 493 PHE cc_start: 0.8412 (m-80) cc_final: 0.7955 (m-80) REVERT: C 628 MET cc_start: 0.8340 (tmm) cc_final: 0.7955 (tmm) REVERT: C 655 MET cc_start: 0.9343 (mmp) cc_final: 0.9089 (mmm) REVERT: D 132 MET cc_start: 0.9275 (mmp) cc_final: 0.8684 (mmm) REVERT: D 136 ASP cc_start: 0.8460 (t70) cc_final: 0.8247 (t0) REVERT: D 142 MET cc_start: 0.7768 (mmt) cc_final: 0.7462 (mmp) REVERT: D 277 LEU cc_start: 0.7978 (mt) cc_final: 0.7753 (mt) REVERT: D 646 TYR cc_start: 0.9108 (t80) cc_final: 0.8742 (t80) REVERT: D 698 ASN cc_start: 0.8095 (t0) cc_final: 0.7710 (t0) REVERT: D 706 MET cc_start: 0.9090 (mmm) cc_final: 0.8803 (mmt) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1249 time to fit residues: 53.4406 Evaluate side-chains 197 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 247 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 263 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 232 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 211 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.072414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.057730 restraints weight = 126128.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059227 restraints weight = 77745.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060247 restraints weight = 56222.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060965 restraints weight = 44942.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061442 restraints weight = 38444.413| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22460 Z= 0.122 Angle : 0.620 11.405 30854 Z= 0.305 Chirality : 0.044 0.203 3810 Planarity : 0.004 0.061 3882 Dihedral : 4.983 60.203 3232 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.32 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.16), residues: 3072 helix: 0.80 (0.16), residues: 1164 sheet: -1.66 (0.23), residues: 468 loop : -1.65 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 36 TYR 0.013 0.001 TYR D 287 PHE 0.024 0.001 PHE A 714 TRP 0.034 0.001 TRP C 752 HIS 0.003 0.001 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (22434) covalent geometry : angle 0.60519 / 0.30 (30800) SS BOND : bond 0.00443 / 0.34 ( 18) SS BOND : angle 2.03073 / 1.30 ( 36) hydrogen bonds : bond 0.03364 / 2.37 ( 926) hydrogen bonds : angle 4.52368 / 3.28 ( 2598) Misc. bond : bond 0.00195 / 0.10 ( 2) link_BETA1-4 : bond 0.00641 / 0.32 ( 2) link_BETA1-4 : angle 1.89507 / 1.01 ( 6) link_NAG-ASN : bond 0.00899 / 0.46 ( 4) link_NAG-ASN : angle 5.93342 / 3.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 493 PHE cc_start: 0.8294 (m-80) cc_final: 0.7876 (m-80) REVERT: A 628 MET cc_start: 0.8352 (tmm) cc_final: 0.8005 (tmm) REVERT: A 655 MET cc_start: 0.9305 (tpp) cc_final: 0.8934 (tpp) REVERT: B 73 MET cc_start: 0.8150 (tpt) cc_final: 0.7891 (tpp) REVERT: B 132 MET cc_start: 0.9253 (mmp) cc_final: 0.8564 (mmm) REVERT: B 134 MET cc_start: 0.8566 (pmm) cc_final: 0.8067 (pmm) REVERT: B 136 ASP cc_start: 0.8571 (t70) cc_final: 0.8281 (t0) REVERT: B 142 MET cc_start: 0.8078 (mmt) cc_final: 0.7782 (mmt) REVERT: B 503 MET cc_start: 0.8994 (ptp) cc_final: 0.8420 (ptt) REVERT: B 612 LEU cc_start: 0.9432 (tp) cc_final: 0.9146 (tp) REVERT: B 646 TYR cc_start: 0.9033 (t80) cc_final: 0.8706 (t80) REVERT: B 698 ASN cc_start: 0.7894 (t0) cc_final: 0.7560 (t0) REVERT: C 153 GLU cc_start: 0.9237 (mp0) cc_final: 0.9004 (mp0) REVERT: C 493 PHE cc_start: 0.8380 (m-80) cc_final: 0.7958 (m-80) REVERT: C 628 MET cc_start: 0.8244 (tmm) cc_final: 0.7992 (tmm) REVERT: D 132 MET cc_start: 0.9271 (mmp) cc_final: 0.8686 (mmm) REVERT: D 142 MET cc_start: 0.7624 (mmt) cc_final: 0.7320 (mmp) REVERT: D 612 LEU cc_start: 0.9412 (tp) cc_final: 0.8897 (tp) REVERT: D 646 TYR cc_start: 0.9092 (t80) cc_final: 0.8778 (t80) REVERT: D 698 ASN cc_start: 0.8067 (t0) cc_final: 0.7704 (t0) REVERT: D 706 MET cc_start: 0.9077 (mmm) cc_final: 0.8796 (mmt) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1260 time to fit residues: 54.9453 Evaluate side-chains 201 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 114 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 130 optimal weight: 0.0370 chunk 260 optimal weight: 30.0000 chunk 289 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 280 optimal weight: 0.0670 chunk 189 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.072940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058246 restraints weight = 126276.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.059768 restraints weight = 78209.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060781 restraints weight = 56539.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.061496 restraints weight = 45293.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.061996 restraints weight = 38768.861| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22460 Z= 0.110 Angle : 0.617 13.619 30854 Z= 0.302 Chirality : 0.044 0.296 3810 Planarity : 0.004 0.061 3882 Dihedral : 4.870 57.792 3232 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.87 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.16), residues: 3072 helix: 0.92 (0.16), residues: 1150 sheet: -1.49 (0.23), residues: 454 loop : -1.59 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 692 TYR 0.013 0.001 TYR D 287 PHE 0.015 0.001 PHE B 241 TRP 0.033 0.001 TRP D 796 HIS 0.003 0.000 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (22434) covalent geometry : angle 0.60295 / 0.30 (30800) SS BOND : bond 0.00702 / 0.56 ( 18) SS BOND : angle 2.03937 / 1.31 ( 36) hydrogen bonds : bond 0.03285 / 2.31 ( 926) hydrogen bonds : angle 4.44474 / 3.23 ( 2598) Misc. bond : bond 0.00200 / 0.10 ( 2) link_BETA1-4 : bond 0.00404 / 0.21 ( 2) link_BETA1-4 : angle 1.90757 / 1.03 ( 6) link_NAG-ASN : bond 0.00893 / 0.46 ( 4) link_NAG-ASN : angle 5.65866 / 3.47 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 GLU cc_start: 0.8836 (tp30) cc_final: 0.8604 (tp30) REVERT: A 230 MET cc_start: 0.8857 (mmm) cc_final: 0.8202 (mmm) REVERT: A 493 PHE cc_start: 0.8283 (m-80) cc_final: 0.7846 (m-80) REVERT: A 628 MET cc_start: 0.8387 (tmm) cc_final: 0.8010 (tmm) REVERT: B 73 MET cc_start: 0.8140 (tpt) cc_final: 0.7898 (tpp) REVERT: B 132 MET cc_start: 0.9231 (mmp) cc_final: 0.8526 (mmm) REVERT: B 134 MET cc_start: 0.8579 (pmm) cc_final: 0.8021 (pmm) REVERT: B 136 ASP cc_start: 0.8575 (t70) cc_final: 0.8322 (t0) REVERT: B 142 MET cc_start: 0.8104 (mmt) cc_final: 0.7763 (mmt) REVERT: B 503 MET cc_start: 0.9049 (ptp) cc_final: 0.8477 (ptt) REVERT: B 609 LEU cc_start: 0.9265 (mm) cc_final: 0.9002 (pp) REVERT: B 612 LEU cc_start: 0.9432 (tp) cc_final: 0.9189 (tp) REVERT: B 646 TYR cc_start: 0.9023 (t80) cc_final: 0.8699 (t80) REVERT: B 698 ASN cc_start: 0.7884 (t0) cc_final: 0.7541 (t0) REVERT: C 153 GLU cc_start: 0.9235 (mp0) cc_final: 0.8989 (mp0) REVERT: C 493 PHE cc_start: 0.8336 (m-80) cc_final: 0.7904 (m-80) REVERT: C 628 MET cc_start: 0.8313 (tmm) cc_final: 0.8022 (tmm) REVERT: D 132 MET cc_start: 0.9275 (mmp) cc_final: 0.8732 (mmm) REVERT: D 142 MET cc_start: 0.7712 (mmt) cc_final: 0.7396 (mmp) REVERT: D 161 MET cc_start: 0.7647 (ptp) cc_final: 0.7250 (ptp) REVERT: D 166 TRP cc_start: 0.8469 (m-90) cc_final: 0.8171 (m-90) REVERT: D 612 LEU cc_start: 0.9412 (tp) cc_final: 0.9002 (tp) REVERT: D 646 TYR cc_start: 0.9096 (t80) cc_final: 0.8718 (t80) REVERT: D 698 ASN cc_start: 0.8052 (t0) cc_final: 0.7690 (t0) REVERT: D 706 MET cc_start: 0.9087 (mmm) cc_final: 0.8797 (mmt) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1245 time to fit residues: 54.7725 Evaluate side-chains 203 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 308 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 chunk 256 optimal weight: 30.0000 chunk 262 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.072489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057893 restraints weight = 127371.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059395 restraints weight = 78901.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.060413 restraints weight = 57037.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061083 restraints weight = 45654.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061596 restraints weight = 39191.685| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22460 Z= 0.126 Angle : 0.627 11.650 30854 Z= 0.307 Chirality : 0.044 0.328 3810 Planarity : 0.004 0.063 3882 Dihedral : 4.898 56.805 3232 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.16), residues: 3072 helix: 0.99 (0.16), residues: 1138 sheet: -1.49 (0.23), residues: 468 loop : -1.51 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 692 TYR 0.012 0.001 TYR D 287 PHE 0.015 0.001 PHE B 241 TRP 0.033 0.001 TRP D 796 HIS 0.003 0.001 HIS C 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22434) covalent geometry : angle 0.61191 / 0.30 (30800) SS BOND : bond 0.00353 / 0.26 ( 18) SS BOND : angle 2.37299 / 1.53 ( 36) hydrogen bonds : bond 0.03267 / 2.30 ( 926) hydrogen bonds : angle 4.44853 / 3.24 ( 2598) Misc. bond : bond 0.00178 / 0.09 ( 2) link_BETA1-4 : bond 0.00667 / 0.34 ( 2) link_BETA1-4 : angle 1.74866 / 0.92 ( 6) link_NAG-ASN : bond 0.00826 / 0.42 ( 4) link_NAG-ASN : angle 5.49676 / 3.40 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.46 seconds wall clock time: 62 minutes 54.87 seconds (3774.87 seconds total)