Starting phenix.real_space_refine on Thu Jun 19 16:36:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6whx_21679/06_2025/6whx_21679.cif Found real_map, /net/cci-nas-00/data/ceres_data/6whx_21679/06_2025/6whx_21679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6whx_21679/06_2025/6whx_21679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6whx_21679/06_2025/6whx_21679.map" model { file = "/net/cci-nas-00/data/ceres_data/6whx_21679/06_2025/6whx_21679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6whx_21679/06_2025/6whx_21679.cif" } resolution = 4.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.019 sd= 1.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 127 5.16 5 Cl 4 4.86 5 C 14733 2.51 5 N 3768 2.21 5 O 4291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22925 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5691 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 32, 'TRANS': 758} Chain breaks: 4 Unresolved non-hydrogen bonds: 566 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 26, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 379 Chain: "B" Number of atoms: 5729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5729 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 588 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 13, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 314 Chain: "C" Number of atoms: 5783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5783 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 32, 'TRANS': 762} Chain breaks: 4 Unresolved non-hydrogen bonds: 516 Unresolved non-hydrogen angles: 625 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 358 Chain: "D" Number of atoms: 5642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5642 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 27, 'TRANS': 756} Chain breaks: 2 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 489 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 18, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 30, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 411 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 13.98, per 1000 atoms: 0.61 Number of scatterers: 22925 At special positions: 0 Unit cell: (134.26, 149.33, 190.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 127 16.00 P 2 15.00 O 4291 8.00 N 3768 7.00 C 14733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.02 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 557 " - pdb=" SG CYS C 831 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 329 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 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=2.03 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 NAG-ASN " NAG A1001 " - " ASN A 159 " " NAG C1001 " - " ASN C 389 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.25 Conformation dependent library (CDL) restraints added in 3.0 seconds 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5888 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 27 sheets defined 38.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 36 through 52 removed outlier: 4.736A pdb=" N GLN A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.631A pdb=" N MET A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 78 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 removed outlier: 4.517A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.933A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.798A pdb=" N VAL A 150 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET A 154 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET A 155 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 157 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.605A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 231 removed outlier: 4.048A pdb=" N GLU A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 4.228A pdb=" N THR A 251 " --> pdb=" O ASP A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 276 through 282 removed outlier: 4.116A pdb=" N LEU A 280 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 314 removed outlier: 4.035A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 479 through 492 removed outlier: 3.720A pdb=" N LEU A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 541 through 546 removed outlier: 3.548A pdb=" N GLN A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 604 removed outlier: 4.049A pdb=" N GLY A 588 " --> pdb=" O TRP A 584 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 594 " --> pdb=" O SER A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 635 removed outlier: 3.823A pdb=" N PHE A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 678 removed outlier: 3.788A pdb=" N ILE A 663 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 734 through 742 removed outlier: 3.991A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLN A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 745 No H-bonds generated for 'chain 'A' and resid 743 through 745' Processing helix chain 'A' and resid 788 through 798 removed outlier: 4.459A pdb=" N GLN A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 801 No H-bonds generated for 'chain 'A' and resid 799 through 801' Processing helix chain 'A' and resid 804 through 813 removed outlier: 3.974A pdb=" N LYS A 811 " --> pdb=" O GLU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 833 removed outlier: 3.860A pdb=" N ASN A 833 " --> pdb=" O THR A 830 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 830 through 833' Processing helix chain 'A' and resid 834 through 856 removed outlier: 4.259A pdb=" N PHE A 838 " --> pdb=" O MET A 834 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'B' and resid 77 through 89 removed outlier: 4.297A pdb=" N ARG B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 4.148A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 164 removed outlier: 4.139A pdb=" N MET B 157 " --> pdb=" O GLN B 153 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 191 removed outlier: 4.022A pdb=" N THR B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 215 through 220 removed outlier: 3.544A pdb=" N LEU B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.724A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 310 removed outlier: 4.095A pdb=" N MET B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 335 through 339 removed outlier: 4.284A pdb=" N TYR B 338 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 467 Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.691A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 522 removed outlier: 3.603A pdb=" N VAL B 522 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 573 removed outlier: 3.683A pdb=" N MET B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 601 through 614 removed outlier: 4.931A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 650 removed outlier: 3.660A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.505A pdb=" N ASN B 694 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 704 removed outlier: 4.075A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 722 Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.514A pdb=" N LEU B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 739 " --> pdb=" O VAL B 735 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 787 removed outlier: 4.460A pdb=" N GLN B 782 " --> pdb=" O LEU B 778 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 787 " --> pdb=" O LEU B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 Processing helix chain 'B' and resid 814 through 819 removed outlier: 4.217A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 844 removed outlier: 3.526A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 4.080A pdb=" N GLU C 39 " --> pdb=" O ARG C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 48 Processing helix chain 'C' and resid 70 through 77 removed outlier: 4.327A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.665A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.671A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 4.248A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.701A pdb=" N ALA C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 257 removed outlier: 3.539A pdb=" N THR C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 301 through 312 removed outlier: 4.003A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 346 through 349 removed outlier: 3.571A pdb=" N SER C 349 " --> pdb=" O LEU C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 478 through 492 removed outlier: 4.025A pdb=" N ARG C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR C 490 " --> pdb=" O LYS C 486 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N MET C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 492 " --> pdb=" O ALA C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.689A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 526 " --> pdb=" O MET C 522 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 527 " --> pdb=" O MET C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 582 through 603 removed outlier: 3.718A pdb=" N LEU C 586 " --> pdb=" O THR C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 634 removed outlier: 4.930A pdb=" N PHE C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 674 removed outlier: 3.980A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 652 " --> pdb=" O PHE C 648 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 659 " --> pdb=" O MET C 655 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 665 " --> pdb=" O ALA C 661 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 695 removed outlier: 3.643A pdb=" N ARG C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 695 " --> pdb=" O PRO C 691 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 690 through 695' Processing helix chain 'C' and resid 709 through 716 removed outlier: 3.809A pdb=" N ARG C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 720 through 728 removed outlier: 4.002A pdb=" N HIS C 726 " --> pdb=" O THR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 741 Processing helix chain 'C' and resid 756 through 761 removed outlier: 3.681A pdb=" N GLU C 760 " --> pdb=" O VAL C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 799 removed outlier: 3.540A pdb=" N VAL C 793 " --> pdb=" O TRP C 789 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU C 798 " --> pdb=" O SER C 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 814 Processing helix chain 'C' and resid 834 through 850 removed outlier: 4.107A pdb=" N PHE C 838 " --> pdb=" O MET C 834 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 848 " --> pdb=" O GLY C 844 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 858 Processing helix chain 'D' and resid 77 through 92 Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.776A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 4.466A pdb=" N MET D 157 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 188 removed outlier: 5.232A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS D 185 " --> pdb=" O ASP D 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 233 through 245 Processing helix chain 'D' and resid 288 through 311 removed outlier: 3.640A pdb=" N MET D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.579A pdb=" N ARG D 337 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 4.347A pdb=" N SER D 426 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 447 removed outlier: 3.597A pdb=" N ASP D 447 " --> pdb=" O ASN D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 473 removed outlier: 3.633A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 removed outlier: 5.026A pdb=" N VAL D 501 " --> pdb=" O MET D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 579 removed outlier: 4.044A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET D 561 " --> pdb=" O CYS D 557 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR D 579 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 removed outlier: 3.755A pdb=" N TRP D 610 " --> pdb=" O ILE D 606 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 629 No H-bonds generated for 'chain 'D' and resid 627 through 629' Processing helix chain 'D' and resid 630 through 650 removed outlier: 4.019A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 removed outlier: 3.795A pdb=" N ARG D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 696 Processing helix chain 'D' and resid 699 through 707 removed outlier: 4.136A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 704 " --> pdb=" O ALA D 700 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY D 707 " --> pdb=" O HIS D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 720 removed outlier: 3.665A pdb=" N ASP D 716 " --> pdb=" O GLY D 713 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU D 718 " --> pdb=" O ASP D 715 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 719 " --> pdb=" O ASP D 716 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 4.361A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 785 removed outlier: 3.916A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 797 Processing helix chain 'D' and resid 814 through 844 removed outlier: 3.900A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N MET D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU D 841 " --> pdb=" O ILE D 837 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 5.943A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 240 Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 292 removed outlier: 4.110A pdb=" N GLN A 291 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 374 " --> pdb=" O GLY A 386 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY A 386 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.376A pdb=" N ILE A 421 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 535 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA A 536 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY A 780 " --> pdb=" O ALA A 536 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 456 through 457 Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 511 removed outlier: 3.860A pdb=" N VAL A 511 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 753 removed outlier: 3.817A pdb=" N TRP A 752 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR A 560 " --> pdb=" O TRP A 752 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.164A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 171 through 173 removed outlier: 6.210A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 227 through 229 removed outlier: 7.171A pdb=" N ILE B 228 " --> pdb=" O ILE B 257 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 278 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 258 " --> pdb=" O ILE B 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 364 through 367 removed outlier: 6.241A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.667A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS B 457 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU B 480 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLN B 437 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR B 479 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 510 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB5, first strand: chain 'B' and resid 532 through 534 removed outlier: 7.016A pdb=" N THR B 532 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N SER B 759 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 538 through 539 removed outlier: 3.761A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 Processing sheet with id=AB8, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.973A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'C' and resid 290 through 292 removed outlier: 3.513A pdb=" N GLN C 291 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 498 through 499 removed outlier: 6.029A pdb=" N ILE C 421 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 422 " --> pdb=" O MET C 533 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET C 783 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 549 " --> pdb=" O MET C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 455 through 459 removed outlier: 3.530A pdb=" N VAL C 455 " --> pdb=" O CYS C 476 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 559 through 560 removed outlier: 3.845A pdb=" N TRP C 752 " --> pdb=" O THR C 560 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.899A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 72 through 73 removed outlier: 6.500A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA D 100 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 42 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 124 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 227 through 228 removed outlier: 6.542A pdb=" N ILE D 228 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 365 " --> pdb=" O SER D 279 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER D 281 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.562A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU D 480 " --> pdb=" O PRO D 435 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN D 437 " --> pdb=" O LEU D 480 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 683 through 684 removed outlier: 3.646A pdb=" N GLY D 684 " --> pdb=" O ALA D 728 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 680 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.05 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7372 1.34 - 1.46: 5627 1.46 - 1.58: 10190 1.58 - 1.70: 2 1.70 - 1.82: 216 Bond restraints: 23407 Sorted by residual: bond pdb=" C1 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.851 1.661 0.190 2.00e-02 2.50e+03 9.05e+01 bond pdb=" C1 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.851 1.662 0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" O3 QGP B 901 " pdb=" P QGP B 901 " ideal model delta sigma weight residual 1.629 1.473 0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" O3 QGP D 901 " pdb=" P QGP D 901 " ideal model delta sigma weight residual 1.629 1.475 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" C1 QGP B 901 " pdb=" C5 QGP B 901 " ideal model delta sigma weight residual 1.503 1.392 0.111 2.00e-02 2.50e+03 3.07e+01 ... (remaining 23402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 31851 4.10 - 8.21: 139 8.21 - 12.31: 1 12.31 - 16.41: 0 16.41 - 20.51: 2 Bond angle restraints: 31993 Sorted by residual: angle pdb=" C VAL D 422 " pdb=" N ASP D 423 " pdb=" CA ASP D 423 " ideal model delta sigma weight residual 122.48 140.93 -18.45 1.77e+00 3.19e-01 1.09e+02 angle pdb=" N VAL D 776 " pdb=" CA VAL D 776 " pdb=" C VAL D 776 " ideal model delta sigma weight residual 113.53 105.41 8.12 9.80e-01 1.04e+00 6.87e+01 angle pdb=" N VAL B 735 " pdb=" CA VAL B 735 " pdb=" C VAL B 735 " ideal model delta sigma weight residual 113.43 107.19 6.24 1.09e+00 8.42e-01 3.27e+01 angle pdb=" N VAL C 742 " pdb=" CA VAL C 742 " pdb=" C VAL C 742 " ideal model delta sigma weight residual 113.42 107.35 6.07 1.17e+00 7.31e-01 2.69e+01 angle pdb=" N ILE A 275 " pdb=" CA ILE A 275 " pdb=" C ILE A 275 " ideal model delta sigma weight residual 111.91 107.32 4.59 8.90e-01 1.26e+00 2.66e+01 ... (remaining 31988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.80: 12452 18.80 - 37.59: 1108 37.59 - 56.39: 176 56.39 - 75.19: 24 75.19 - 93.98: 23 Dihedral angle restraints: 13783 sinusoidal: 4661 harmonic: 9122 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 329 " pdb=" CB CYS C 329 " ideal model delta sinusoidal sigma weight residual -86.00 -3.02 -82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CA ILE A 322 " pdb=" C ILE A 322 " pdb=" N THR A 323 " pdb=" CA THR A 323 " ideal model delta harmonic sigma weight residual -180.00 -140.02 -39.98 0 5.00e+00 4.00e-02 6.39e+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 93.00 155.87 -62.87 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 13780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2868 0.054 - 0.108: 828 0.108 - 0.161: 124 0.161 - 0.215: 11 0.215 - 0.269: 1 Chirality restraints: 3832 Sorted by residual: chirality pdb=" CB ILE A 287 " pdb=" CA ILE A 287 " pdb=" CG1 ILE A 287 " pdb=" CG2 ILE A 287 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA VAL C 141 " pdb=" N VAL C 141 " pdb=" C VAL C 141 " pdb=" CB VAL C 141 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB ILE B 50 " pdb=" CA ILE B 50 " pdb=" CG1 ILE B 50 " pdb=" CG2 ILE B 50 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 3829 not shown) Planarity restraints: 4058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 105 " -0.060 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO C 106 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 679 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.94e+00 pdb=" N PRO B 680 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 680 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 680 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 787 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO C 788 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 788 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 788 " 0.037 5.00e-02 4.00e+02 ... (remaining 4055 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 422 2.62 - 3.19: 22672 3.19 - 3.76: 32494 3.76 - 4.33: 42937 4.33 - 4.90: 65751 Nonbonded interactions: 164276 Sorted by model distance: nonbonded pdb=" O ILE B 115 " pdb=" OG1 THR B 119 " model vdw 2.048 3.040 nonbonded pdb=" OG SER D 131 " pdb=" O PHE D 146 " model vdw 2.102 3.040 nonbonded pdb=" OG1 THR D 343 " pdb=" O ARG D 347 " model vdw 2.103 3.040 nonbonded pdb=" OH TYR B 167 " pdb=" OG1 THR B 428 " model vdw 2.112 3.040 nonbonded pdb=" O GLY C 328 " pdb=" ND2 ASN C 332 " model vdw 2.118 3.120 ... (remaining 164271 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 36 or (resid 37 through 45 and (na \ me N or name CA or name C or name O or name CB )) or resid 46 through 47 or (res \ id 48 through 49 and (name N or name CA or name C or name O or name CB )) or res \ id 50 through 58 or (resid 59 and (name N or name CA or name C or name O or name \ CB )) or resid 60 or (resid 61 through 62 and (name N or name CA or name C or n \ ame O or name CB )) or resid 63 through 66 or (resid 67 and (name N or name CA o \ r name C or name O or name CB )) or resid 68 through 79 or (resid 80 through 81 \ and (name N or name CA or name C or name O or name CB )) or resid 82 through 86 \ or (resid 87 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 8 through 114 or (resid 115 and (name N or name CA or name C or name O or name C \ B )) or resid 116 through 145 or (resid 146 and (name N or name CA or name C or \ name O or name CB )) or resid 147 through 158 or (resid 159 and (name N or name \ CA or name C or name O or name CB )) or resid 160 through 161 or (resid 162 and \ (name N or name CA or name C or name O or name CB )) or resid 163 through 168 or \ (resid 169 through 170 and (name N or name CA or name C or name O or name CB )) \ or resid 171 through 178 or (resid 179 and (name N or name CA or name C or name \ O or name CB )) or resid 180 through 230 or (resid 231 through 232 and (name N \ or name CA or name C or name O or name CB )) or resid 233 or (resid 234 and (nam \ e N or name CA or name C or name O or name CB )) or resid 235 through 265 or (re \ sid 266 and (name N or name CA or name C or name O or name CB )) or resid 267 th \ rough 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) \ or resid 276 through 277 or (resid 278 through 283 and (name N or name CA or na \ me C or name O or name CB )) or resid 284 through 291 or (resid 292 through 293 \ and (name N or name CA or name C or name O or name CB )) or resid 294 through 31 \ 3 or (resid 314 through 315 and (name N or name CA or name C or name O or name C \ B )) or resid 316 through 329 or (resid 330 and (name N or name CA or name C or \ name O or name CB )) or resid 331 through 333 or (resid 334 and (name N or name \ CA or name C or name O or name CB )) or resid 335 through 342 or (resid 343 thro \ ugh 344 and (name N or name CA or name C or name O or name CB )) or resid 345 th \ rough 395 or (resid 396 through 399 and (name N or name CA or name C or name O o \ r name CB )) or resid 400 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 432 or (resid 433 and (name N \ or name CA or name C or name O or name CB )) or resid 434 through 509 or (resid \ 510 and (name N or name CA or name C or name O or name CB )) or resid 511 throug \ h 521 or (resid 522 and (name N or name CA or name C or name O or name CB )) or \ resid 523 through 542 or (resid 543 and (name N or name CA or name C or name O o \ r name CB )) or resid 544 through 575 or (resid 576 and (name N or name CA or na \ me C or name O or name CB )) or resid 577 through 583 or (resid 584 and (name N \ or name CA or name C or name O or name CB )) or resid 585 through 681 or (resid \ 682 through 684 and (name N or name CA or name C or name O or name CB )) or resi \ d 685 through 724 or (resid 725 and (name N or name CA or name C or name O or na \ me CB )) or resid 726 through 789 or (resid 790 and (name N or name CA or name C \ or name O or name CB )) or resid 791 through 821 or (resid 822 and (name N or n \ ame CA or name C or name O or name CB )) or resid 823 through 862 or resid 1001) \ ) selection = (chain 'C' and (resid 25 through 38 or (resid 39 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 through 49 and (na \ me N or name CA or name C or name O or name CB )) or resid 50 through 72 or (res \ id 73 through 75 and (name N or name CA or name C or name O or name CB )) or res \ id 76 through 108 or (resid 109 and (name N or name CA or name C or name O or na \ me CB )) or resid 110 through 129 or (resid 130 through 131 and (name N or name \ CA or name C or name O or name CB )) or resid 132 through 136 or (resid 137 and \ (name N or name CA or name C or name O or name CB )) or resid 138 or (resid 139 \ and (name N or name CA or name C or name O or name CB )) or resid 140 through 15 \ 5 or (resid 156 and (name N or name CA or name C or name O or name CB )) or resi \ d 157 through 180 or (resid 181 and (name N or name CA or name C or name O or na \ me CB )) or resid 182 through 184 or (resid 185 and (name N or name CA or name C \ or name O or name CB )) or resid 186 through 190 or resid 208 through 210 or (r \ esid 211 through 212 and (name N or name CA or name C or name O or name CB )) or \ resid 213 through 221 or (resid 222 through 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225 through 253 or (resid 254 through 262 and \ (name N or name CA or name C or name O or name CB )) or resid 263 through 284 o \ r (resid 285 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 86 through 292 or (resid 293 and (name N or name CA or name C or name O or name \ CB )) or resid 294 through 303 or (resid 304 through 305 and (name N or name CA \ or name C or name O or name CB )) or resid 306 through 310 or (resid 311 through \ 312 and (name N or name CA or name C or name O or name CB )) or resid 313 throu \ gh 323 or (resid 324 and (name N or name CA or name C or name O or name CB )) or \ resid 325 through 336 or (resid 337 and (name N or name CA or name C or name O \ or name CB )) or resid 338 through 357 or (resid 358 and (name N or name CA or n \ ame C or name O or name CB )) or resid 359 or (resid 360 and (name N or name CA \ or name C or name O or name CB )) or resid 361 through 367 or (resid 368 and (na \ me N or name CA or name C or name O or name CB )) or resid 369 through 374 or (r \ esid 375 and (name N or name CA or name C or name O or name CB )) or resid 376 t \ hrough 377 or (resid 378 through 381 and (name N or name CA or name C or name O \ or name CB )) or resid 382 through 390 or (resid 391 through 392 and (name N or \ name CA or name C or name O or name CB )) or resid 393 through 410 or (resid 411 \ and (name N or name CA or name C or name O or name CB )) or resid 412 through 4 \ 14 or (resid 415 and (name N or name CA or name C or name O or name CB )) or res \ id 416 through 417 or (resid 418 and (name N or name CA or name C or name O or n \ ame CB )) or resid 419 through 435 or (resid 436 and (name N or name CA or name \ C or name O or name CB )) or resid 437 through 443 or (resid 444 and (name N or \ name CA or name C or name O or name CB )) or resid 445 through 447 or (resid 448 \ and (name N or name CA or name C or name O or name CB )) or resid 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 451 throu \ gh 452 or (resid 453 and (name N or name CA or name C or name O or name CB )) or \ resid 454 through 461 or (resid 462 through 463 and (name N or name CA or name \ C or name O or name CB )) or resid 464 through 486 or (resid 487 through 488 and \ (name N or name CA or name C or name O or name CB )) or resid 489 through 490 o \ r (resid 491 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 92 through 503 or (resid 504 and (name N or name CA or name C or name O or name \ CB )) or resid 505 through 507 or (resid 508 through 510 and (name N or name CA \ or name C or name O or name CB )) or resid 511 through 548 or (resid 549 and (na \ me N or name CA or name C or name O or name CB )) or resid 550 through 565 or (r \ esid 566 and (name N or name CA or name C or name O or name CB )) or resid 567 t \ hrough 568 or (resid 569 and (name N or name CA or name C or name O or name CB ) \ ) or resid 570 through 571 or (resid 572 and (name N or name CA or name C or nam \ e O or name CB )) or resid 573 through 641 or (resid 642 and (name N or name CA \ or name C or name O or name CB )) or resid 643 through 691 or (resid 692 and (na \ me N or name CA or name C or name O or name CB )) or resid 693 through 698 or (r \ esid 699 and (name N or name CA or name C or name O or name CB )) or resid 700 t \ hrough 714 or (resid 715 through 716 and (name N or name CA or name C or name O \ or name CB )) or resid 717 through 723 or (resid 724 through 725 and (name N or \ name CA or name C or name O or name CB )) or resid 726 through 728 or (resid 729 \ and (name N or name CA or name C or name O or name CB )) or resid 730 through 7 \ 42 or (resid 743 and (name N or name CA or name C or name O or name CB )) or res \ id 744 through 784 or (resid 785 and (name N or name CA or name C or name O or n \ ame CB )) or resid 786 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 816 or (resid 817 through 818 and \ (name N or name CA or name C or name O or name CB )) or resid 819 through 862 o \ r resid 1001)) } ncs_group { reference = (chain 'B' and (resid 34 or (resid 35 and (name N or name CA or name C or name O \ or name CB )) or resid 36 through 43 or (resid 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 through 58 or (resid 59 through 62 and ( \ name N or name CA or name C or name O or name CB )) or resid 63 through 66 or (r \ esid 67 and (name N or name CA or name C or name O or name CB )) or resid 68 or \ (resid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 t \ hrough 72 or (resid 73 through 75 and (name N or name CA or name C or name O or \ name CB )) or resid 76 or (resid 77 and (name N or name CA or name C or name O o \ r name CB )) or resid 78 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB )) or resid 85 through 94 or (resid 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 101 or (resid 102 and \ (name N or name CA or name C or name O or name CB )) or resid 103 or (resid 104 \ through 107 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 08 through 109 or (resid 110 and (name N or name CA or name C or name O or name \ CB )) or resid 111 through 112 or (resid 113 and (name N or name CA or name C or \ name O or name CB )) or resid 114 through 119 or (resid 120 and (name N or name \ CA or name C or name O or name CB )) or resid 121 through 137 or (resid 138 thr \ ough 139 and (name N or name CA or name C or name O or name CB )) or resid 140 t \ hrough 200 or (resid 201 and (name N or name CA or name C or name O or name CB ) \ ) or resid 202 through 221 or (resid 222 and (name N or name CA or name C or nam \ e O or name CB )) or resid 223 through 234 or (resid 235 through 237 and (name N \ or name CA or name C or name O or name CB )) or resid 238 through 241 or (resid \ 242 and (name N or name CA or name C or name O or name CB )) or resid 243 throu \ gh 251 or (resid 252 and (name N or name CA or name C or name O or name CB )) or \ resid 253 through 271 or (resid 272 and (name N or name CA or name C or name O \ or name CB )) or resid 273 through 283 or (resid 284 and (name N or name CA or n \ ame C or name O or name CB )) or resid 285 through 286 or (resid 287 and (name N \ or name CA or name C or name O or name CB )) or resid 288 through 325 or (resid \ 326 through 331 and (name N or name CA or name C or name O or name CB )) or res \ id 332 through 381 or (resid 382 and (name N or name CA or name C or name O or n \ ame CB )) or resid 383 through 394 or (resid 403 and (name N or name CA or name \ C or name O or name CB )) or resid 404 through 411 or (resid 412 through 414 and \ (name N or name CA or name C or name O or name CB )) or resid 415 through 419 o \ r (resid 420 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 21 through 422 or (resid 423 and (name N or name CA or name C or name O or name \ CB )) or resid 424 or (resid 425 and (name N or name CA or name C or name O or n \ ame CB )) or resid 426 through 445 or (resid 446 through 449 and (name N or name \ CA or name C or name O or name CB )) or resid 450 through 451 or (resid 452 and \ (name N or name CA or name C or name O or name CB )) or resid 453 through 454 o \ r (resid 455 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 56 through 472 or (resid 473 and (name N or name CA or name C or name O or name \ CB )) or resid 474 through 516 or (resid 517 and (name N or name CA or name C or \ name O or name CB )) or resid 518 through 539 or (resid 540 and (name N or name \ CA or name C or name O or name CB )) or resid 541 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 552 \ and (name N or name CA or name C or name O or name CB )) or resid 553 through 5 \ 62 or (resid 563 and (name N or name CA or name C or name O or name CB )) or res \ id 564 through 621 or (resid 622 and (name N or name CA or name C or name O or n \ ame CB )) or resid 623 through 656 or (resid 657 and (name N or name CA or name \ C or name O or name CB )) or resid 658 through 669 or (resid 670 through 671 and \ (name N or name CA or name C or name O or name CB )) or resid 672 or (resid 673 \ and (name N or name CA or name C or name O or name CB )) or resid 674 through 7 \ 10 or (resid 711 through 712 and (name N or name CA or name C or name O or name \ CB )) or resid 713 through 715 or (resid 716 through 717 and (name N or name CA \ or name C or name O or name CB )) or resid 718 or (resid 719 and (name N or name \ CA or name C or name O or name CB )) or resid 720 through 726 or (resid 727 thr \ ough 728 and (name N or name CA or name C or name O or name CB )) or resid 729 t \ hrough 741 or (resid 742 through 744 and (name N or name CA or name C or name O \ or name CB )) or resid 745 through 746 or (resid 747 and (name N or name CA or n \ ame C or name O or name CB )) or resid 748 through 801 or (resid 802 and (name N \ or name CA or name C or name O or name CB )) or resid 803 through 805 or (resid \ 806 through 807 and (name N or name CA or name C or name O or name CB )) or res \ id 808 through 816 or (resid 817 through 819 and (name N or name CA or name C or \ name O or name CB )) or resid 820 through 822 or (resid 823 and (name N or name \ CA or name C or name O or name CB )) or resid 824 through 838 or (resid 839 and \ (name N or name CA or name C or name O or name CB )) or resid 840 through 845 o \ r resid 901)) selection = (chain 'D' and (resid 34 through 46 or (resid 47 and (name N or name CA or name \ C or name O or name CB )) or resid 48 through 51 or (resid 52 through 62 and (na \ me N or name CA or name C or name O or name CB )) or resid 63 through 64 or (res \ id 65 and (name N or name CA or name C or name O or name CB )) or resid 66 throu \ gh 90 or (resid 91 through 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 117 or (resid 118 and (name N or name CA or name C or \ name O or name CB )) or resid 119 through 126 or (resid 127 and (name N or name \ CA or name C or name O or name CB )) or resid 128 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 through 199 o \ r (resid 200 through 201 and (name N or name CA or name C or name O or name CB ) \ ) or resid 202 through 205 or (resid 206 through 207 and (name N or name CA or n \ ame C or name O or name CB )) or resid 208 through 209 or (resid 210 through 211 \ and (name N or name CA or name C or name O or name CB )) or resid 212 through 2 \ 18 or (resid 219 and (name N or name CA or name C or name O or name CB )) or res \ id 220 through 281 or (resid 282 through 284 and (name N or name CA or name C or \ name O or name CB )) or resid 285 through 309 or (resid 310 and (name N or name \ CA or name C or name O or name CB )) or resid 311 through 313 or (resid 314 and \ (name N or name CA or name C or name O or name CB )) or resid 315 through 321 o \ r (resid 322 through 331 and (name N or name CA or name C or name O or name CB ) \ ) or resid 332 or (resid 333 and (name N or name CA or name C or name O or name \ CB )) or resid 334 through 336 or (resid 337 and (name N or name CA or name C or \ name O or name CB )) or resid 338 through 343 or (resid 344 through 345 and (na \ me N or name CA or name C or name O or name CB )) or resid 346 or (resid 347 and \ (name N or name CA or name C or name O or name CB )) or resid 348 or (resid 349 \ and (name N or name CA or name C or name O or name CB )) or resid 350 through 3 \ 68 or (resid 369 through 370 and (name N or name CA or name C or name O or name \ CB )) or resid 371 through 377 or (resid 378 and (name N or name CA or name C or \ name O or name CB )) or resid 379 through 386 or (resid 387 and (name N or name \ CA or name C or name O or name CB )) or resid 388 through 484 or (resid 485 and \ (name N or name CA or name C or name O or name CB )) or resid 486 through 487 o \ r (resid 488 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 89 through 623 or (resid 624 and (name N or name CA or name C or name O or name \ CB )) or resid 625 through 628 or (resid 629 and (name N or name CA or name C or \ name O or name CB )) or resid 630 through 668 or (resid 669 through 671 and (na \ me N or name CA or name C or name O or name CB )) or resid 672 through 691 or (r \ esid 692 and (name N or name CA or name C or name O or name CB )) or resid 693 t \ hrough 698 or (resid 699 through 700 and (name N or name CA or name C or name O \ or name CB )) or resid 701 through 804 or (resid 805 through 807 and (name N or \ name CA or name C or name O or name CB )) or resid 808 through 835 or (resid 836 \ and (name N or name CA or name C or name O or name CB )) or resid 837 through 8 \ 41 or (resid 842 through 845 and (name N or name CA or name C or name O or name \ CB )) or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 52.310 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 : 0.007 0.190 23427 Z= 0.323 Angle : 0.869 20.514 32031 Z= 0.489 Chirality : 0.049 0.269 3832 Planarity : 0.006 0.091 4056 Dihedral : 15.015 93.984 7847 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 19.41 % Favored : 80.56 % Rotamer: Outliers : 0.13 % Allowed : 12.47 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.12), residues: 3122 helix: -3.16 (0.12), residues: 990 sheet: -4.03 (0.23), residues: 299 loop : -4.06 (0.12), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 166 HIS 0.017 0.002 HIS B 486 PHE 0.027 0.002 PHE B 169 TYR 0.022 0.002 TYR D 322 ARG 0.003 0.000 ARG B 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 2) link_NAG-ASN : angle 3.41273 ( 6) hydrogen bonds : bond 0.22287 ( 680) hydrogen bonds : angle 8.80779 ( 1881) SS BOND : bond 0.00319 ( 16) SS BOND : angle 1.28722 ( 32) covalent geometry : bond 0.00682 (23407) covalent geometry : angle 0.86715 (31993) Misc. bond : bond 0.00546 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 382 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.4974 (t70) cc_final: 0.4499 (t-170) REVERT: A 693 LEU cc_start: 0.7328 (tp) cc_final: 0.7060 (tp) REVERT: A 783 MET cc_start: 0.4813 (mtm) cc_final: 0.4261 (mtm) REVERT: B 706 MET cc_start: 0.6129 (ttm) cc_final: 0.5808 (mtp) REVERT: C 116 ILE cc_start: 0.8004 (mt) cc_final: 0.7549 (mt) REVERT: C 415 MET cc_start: 0.5706 (ttm) cc_final: 0.5236 (ttm) REVERT: C 428 PRO cc_start: 0.8243 (Cg_endo) cc_final: 0.7826 (Cg_exo) REVERT: C 806 MET cc_start: 0.6086 (mmm) cc_final: 0.5646 (tpp) REVERT: D 705 TYR cc_start: 0.6637 (t80) cc_final: 0.6436 (t80) REVERT: D 735 VAL cc_start: 0.8176 (t) cc_final: 0.7917 (t) outliers start: 3 outliers final: 2 residues processed: 384 average time/residue: 0.3093 time to fit residues: 191.8606 Evaluate side-chains 283 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 81 optimal weight: 0.2980 chunk 160 optimal weight: 30.0000 chunk 127 optimal weight: 0.6980 chunk 246 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 285 optimal weight: 7.9990 overall best weight: 4.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 426 GLN A 492 GLN A 530 GLN A 542 ASN A 637 ASN A 726 HIS A 731 ASN ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN C 70 ASN C 294 ASN C 425 HIS C 426 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN C 717 GLN C 730 HIS D 224 GLN D 359 HIS D 495 ASN ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN D 775 GLN D 803 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.119789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.099771 restraints weight = 62600.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.103112 restraints weight = 37610.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.104246 restraints weight = 24209.469| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23427 Z= 0.203 Angle : 0.735 17.745 32031 Z= 0.380 Chirality : 0.048 0.226 3832 Planarity : 0.006 0.084 4056 Dihedral : 7.932 63.448 3367 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.29 % Favored : 86.64 % Rotamer: Outliers : 0.22 % Allowed : 5.79 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.13), residues: 3122 helix: -2.06 (0.14), residues: 1020 sheet: -3.57 (0.25), residues: 292 loop : -3.57 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 268 HIS 0.008 0.002 HIS B 486 PHE 0.021 0.002 PHE B 146 TYR 0.021 0.002 TYR C 114 ARG 0.005 0.000 ARG B 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 2) link_NAG-ASN : angle 2.96247 ( 6) hydrogen bonds : bond 0.05402 ( 680) hydrogen bonds : angle 6.27020 ( 1881) SS BOND : bond 0.00476 ( 16) SS BOND : angle 1.41966 ( 32) covalent geometry : bond 0.00465 (23407) covalent geometry : angle 0.73330 (31993) Misc. bond : bond 0.00274 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 373 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8207 (mmp) cc_final: 0.7765 (mmm) REVERT: A 522 MET cc_start: 0.8769 (ptm) cc_final: 0.8548 (ptm) REVERT: A 577 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7444 (tt0) REVERT: A 628 MET cc_start: 0.8534 (tmm) cc_final: 0.8028 (tmm) REVERT: B 99 PHE cc_start: 0.7958 (t80) cc_final: 0.7476 (t80) REVERT: B 654 MET cc_start: 0.7348 (mmp) cc_final: 0.7128 (mmp) REVERT: B 706 MET cc_start: 0.8347 (ttm) cc_final: 0.8062 (mtp) REVERT: B 742 ARG cc_start: 0.8586 (ttm170) cc_final: 0.8322 (ttm170) REVERT: B 789 MET cc_start: 0.9125 (tpt) cc_final: 0.8765 (tpt) REVERT: B 822 PHE cc_start: 0.7138 (m-80) cc_final: 0.6726 (m-80) REVERT: C 138 LEU cc_start: 0.8602 (tp) cc_final: 0.8258 (tp) REVERT: C 415 MET cc_start: 0.5227 (ttm) cc_final: 0.4796 (ttm) REVERT: C 428 PRO cc_start: 0.9211 (Cg_endo) cc_final: 0.8844 (Cg_exo) REVERT: C 491 MET cc_start: 0.8101 (mpp) cc_final: 0.7781 (mpp) REVERT: C 575 PHE cc_start: 0.8568 (p90) cc_final: 0.8347 (p90) REVERT: C 577 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8045 (tm-30) REVERT: C 628 MET cc_start: 0.6717 (tmm) cc_final: 0.6407 (tmm) REVERT: C 655 MET cc_start: 0.6881 (ttm) cc_final: 0.6646 (ttm) REVERT: C 662 MET cc_start: 0.9179 (tmm) cc_final: 0.8869 (tmm) REVERT: C 727 MET cc_start: 0.8806 (mtp) cc_final: 0.8593 (mtm) REVERT: C 758 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7848 (mt-10) REVERT: C 839 MET cc_start: 0.5667 (tpt) cc_final: 0.5063 (tpt) REVERT: D 299 ILE cc_start: 0.9258 (mt) cc_final: 0.9024 (mt) REVERT: D 358 MET cc_start: 0.8127 (mmm) cc_final: 0.7742 (mmm) REVERT: D 505 ARG cc_start: 0.8366 (mtt180) cc_final: 0.8053 (mtt90) REVERT: D 629 LYS cc_start: 0.8383 (tttt) cc_final: 0.7894 (tttt) REVERT: D 641 ILE cc_start: 0.8654 (tp) cc_final: 0.8321 (tp) REVERT: D 654 MET cc_start: 0.8531 (mmm) cc_final: 0.8219 (mmm) outliers start: 5 outliers final: 0 residues processed: 378 average time/residue: 0.2773 time to fit residues: 177.1723 Evaluate side-chains 289 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 73 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 219 optimal weight: 0.0770 chunk 54 optimal weight: 6.9990 chunk 119 optimal weight: 30.0000 chunk 161 optimal weight: 0.0270 chunk 220 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN C 542 ASN C 730 HIS C 801 HIS ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102431 restraints weight = 61323.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105004 restraints weight = 36939.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.106816 restraints weight = 25930.555| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23427 Z= 0.138 Angle : 0.650 15.059 32031 Z= 0.335 Chirality : 0.046 0.230 3832 Planarity : 0.005 0.088 4056 Dihedral : 6.888 61.541 3367 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.79 % Favored : 89.17 % Rotamer: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.14), residues: 3122 helix: -1.34 (0.16), residues: 1020 sheet: -3.29 (0.27), residues: 284 loop : -3.09 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 166 HIS 0.008 0.001 HIS C 801 PHE 0.021 0.002 PHE A 775 TYR 0.019 0.001 TYR C 388 ARG 0.003 0.000 ARG C 776 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 2) link_NAG-ASN : angle 2.70563 ( 6) hydrogen bonds : bond 0.04206 ( 680) hydrogen bonds : angle 5.45127 ( 1881) SS BOND : bond 0.00315 ( 16) SS BOND : angle 1.56427 ( 32) covalent geometry : bond 0.00316 (23407) covalent geometry : angle 0.64787 (31993) Misc. bond : bond 0.00290 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8039 (mmp) cc_final: 0.7503 (mmm) REVERT: A 628 MET cc_start: 0.8538 (tmm) cc_final: 0.7700 (tmm) REVERT: A 693 LEU cc_start: 0.7987 (tp) cc_final: 0.7746 (tp) REVERT: A 748 HIS cc_start: 0.7655 (t-90) cc_final: 0.7340 (t-170) REVERT: B 99 PHE cc_start: 0.7781 (t80) cc_final: 0.7354 (t80) REVERT: B 190 ILE cc_start: 0.7832 (tt) cc_final: 0.7288 (tt) REVERT: B 249 LEU cc_start: 0.8278 (mm) cc_final: 0.7864 (tt) REVERT: B 307 MET cc_start: 0.5845 (mmm) cc_final: 0.5247 (tpp) REVERT: B 374 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7906 (tm-30) REVERT: B 706 MET cc_start: 0.8213 (ttm) cc_final: 0.7759 (mtp) REVERT: B 822 PHE cc_start: 0.7064 (m-80) cc_final: 0.6754 (m-80) REVERT: C 128 TYR cc_start: 0.8066 (m-80) cc_final: 0.7721 (m-80) REVERT: C 138 LEU cc_start: 0.8805 (tp) cc_final: 0.8532 (tp) REVERT: C 415 MET cc_start: 0.5157 (ttm) cc_final: 0.4726 (ttm) REVERT: C 491 MET cc_start: 0.8014 (mpp) cc_final: 0.7700 (mpp) REVERT: C 575 PHE cc_start: 0.8525 (p90) cc_final: 0.8260 (p90) REVERT: C 662 MET cc_start: 0.9071 (tmm) cc_final: 0.8771 (tmm) REVERT: C 758 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 839 MET cc_start: 0.5705 (tpt) cc_final: 0.5074 (tpt) REVERT: D 164 TYR cc_start: 0.7736 (m-10) cc_final: 0.7307 (m-10) REVERT: D 165 ASP cc_start: 0.8352 (t0) cc_final: 0.7717 (p0) REVERT: D 358 MET cc_start: 0.8309 (mmm) cc_final: 0.7775 (mmm) REVERT: D 411 LEU cc_start: 0.8174 (mm) cc_final: 0.7968 (mm) REVERT: D 505 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8145 (mtt180) REVERT: D 641 ILE cc_start: 0.8603 (tp) cc_final: 0.8304 (tp) REVERT: D 643 LEU cc_start: 0.8422 (tp) cc_final: 0.7949 (tt) REVERT: D 654 MET cc_start: 0.8363 (mmm) cc_final: 0.8019 (mmm) outliers start: 1 outliers final: 0 residues processed: 411 average time/residue: 0.2772 time to fit residues: 189.2057 Evaluate side-chains 324 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 72 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 295 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 283 optimal weight: 0.0670 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS ** A 801 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 730 HIS ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 694 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.135820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117877 restraints weight = 64310.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.119495 restraints weight = 44139.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120825 restraints weight = 32866.302| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23427 Z= 0.119 Angle : 0.622 15.036 32031 Z= 0.318 Chirality : 0.045 0.222 3832 Planarity : 0.005 0.083 4056 Dihedral : 6.391 61.315 3367 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.67 % Favored : 90.29 % Rotamer: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.14), residues: 3122 helix: -0.93 (0.16), residues: 1032 sheet: -3.07 (0.27), residues: 295 loop : -2.78 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 166 HIS 0.010 0.001 HIS C 801 PHE 0.023 0.001 PHE D 169 TYR 0.026 0.001 TYR C 388 ARG 0.007 0.000 ARG C 743 Details of bonding type rmsd link_NAG-ASN : bond 0.00591 ( 2) link_NAG-ASN : angle 3.29099 ( 6) hydrogen bonds : bond 0.03690 ( 680) hydrogen bonds : angle 5.14686 ( 1881) SS BOND : bond 0.00374 ( 16) SS BOND : angle 1.33486 ( 32) covalent geometry : bond 0.00270 (23407) covalent geometry : angle 0.61972 (31993) Misc. bond : bond 0.00270 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 416 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.7432 (mmp) cc_final: 0.7133 (mmm) REVERT: A 628 MET cc_start: 0.8316 (tmm) cc_final: 0.7589 (tmm) REVERT: A 747 LEU cc_start: 0.8273 (tp) cc_final: 0.8032 (tp) REVERT: B 307 MET cc_start: 0.5994 (mmm) cc_final: 0.5240 (tpp) REVERT: B 746 CYS cc_start: 0.5938 (m) cc_final: 0.5427 (m) REVERT: B 822 PHE cc_start: 0.6907 (m-80) cc_final: 0.6642 (m-80) REVERT: C 47 ASN cc_start: 0.8523 (m110) cc_final: 0.8029 (t0) REVERT: C 79 CYS cc_start: 0.5467 (p) cc_final: 0.5149 (p) REVERT: C 362 ASN cc_start: 0.8765 (p0) cc_final: 0.8524 (p0) REVERT: C 415 MET cc_start: 0.5428 (ttm) cc_final: 0.4976 (ttm) REVERT: C 457 CYS cc_start: 0.3075 (t) cc_final: 0.2235 (t) REVERT: C 491 MET cc_start: 0.8019 (mpp) cc_final: 0.7716 (mpp) REVERT: C 520 ASN cc_start: 0.8024 (p0) cc_final: 0.7571 (t0) REVERT: C 628 MET cc_start: 0.6642 (tmm) cc_final: 0.6346 (tmm) REVERT: C 662 MET cc_start: 0.9062 (tmm) cc_final: 0.8830 (tmm) REVERT: C 839 MET cc_start: 0.6001 (tpt) cc_final: 0.5314 (tpt) REVERT: D 164 TYR cc_start: 0.7605 (m-10) cc_final: 0.7010 (m-10) REVERT: D 165 ASP cc_start: 0.7540 (t0) cc_final: 0.7143 (p0) REVERT: D 497 MET cc_start: 0.8730 (mmp) cc_final: 0.7899 (mmp) REVERT: D 602 ILE cc_start: 0.7045 (pt) cc_final: 0.6690 (tt) REVERT: D 641 ILE cc_start: 0.8677 (tp) cc_final: 0.8358 (tp) REVERT: D 643 LEU cc_start: 0.8499 (tp) cc_final: 0.7905 (tt) REVERT: D 654 MET cc_start: 0.7953 (mmm) cc_final: 0.7730 (mmm) REVERT: D 675 ASN cc_start: 0.7996 (m-40) cc_final: 0.7735 (m-40) REVERT: D 739 MET cc_start: 0.8484 (mmm) cc_final: 0.8060 (mmm) outliers start: 2 outliers final: 0 residues processed: 418 average time/residue: 0.2792 time to fit residues: 197.5331 Evaluate side-chains 321 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 212 optimal weight: 3.9990 chunk 157 optimal weight: 30.0000 chunk 301 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 69 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 GLN ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 385 GLN ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.120426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099864 restraints weight = 62979.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102256 restraints weight = 38697.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103973 restraints weight = 27623.433| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 23427 Z= 0.223 Angle : 0.740 17.741 32031 Z= 0.377 Chirality : 0.048 0.238 3832 Planarity : 0.005 0.086 4056 Dihedral : 6.991 59.524 3367 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.81 % Favored : 86.16 % Rotamer: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.14), residues: 3122 helix: -1.01 (0.16), residues: 1037 sheet: -3.21 (0.28), residues: 278 loop : -2.86 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 166 HIS 0.011 0.002 HIS A 748 PHE 0.027 0.002 PHE C 579 TYR 0.021 0.002 TYR B 479 ARG 0.003 0.000 ARG C 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 2) link_NAG-ASN : angle 3.05704 ( 6) hydrogen bonds : bond 0.04543 ( 680) hydrogen bonds : angle 5.56885 ( 1881) SS BOND : bond 0.00351 ( 16) SS BOND : angle 1.35935 ( 32) covalent geometry : bond 0.00512 (23407) covalent geometry : angle 0.73772 (31993) Misc. bond : bond 0.00349 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 375 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8453 (pp30) cc_final: 0.7587 (pp30) REVERT: A 457 CYS cc_start: 0.5917 (t) cc_final: 0.4706 (t) REVERT: A 576 MET cc_start: 0.8079 (tpp) cc_final: 0.7737 (mmm) REVERT: A 628 MET cc_start: 0.8628 (tmm) cc_final: 0.7920 (tmm) REVERT: A 693 LEU cc_start: 0.8047 (tp) cc_final: 0.7768 (tp) REVERT: A 723 MET cc_start: 0.9030 (tpp) cc_final: 0.8806 (tpp) REVERT: B 99 PHE cc_start: 0.7911 (t80) cc_final: 0.7492 (t80) REVERT: C 79 CYS cc_start: 0.6267 (p) cc_final: 0.5905 (p) REVERT: C 415 MET cc_start: 0.5120 (ttm) cc_final: 0.4702 (ttm) REVERT: C 457 CYS cc_start: 0.4549 (t) cc_final: 0.3758 (t) REVERT: C 491 MET cc_start: 0.7974 (mpp) cc_final: 0.7671 (mpp) REVERT: C 628 MET cc_start: 0.7029 (tmm) cc_final: 0.6442 (tmm) REVERT: C 662 MET cc_start: 0.8972 (tmm) cc_final: 0.8630 (tmm) REVERT: C 758 GLU cc_start: 0.7908 (mp0) cc_final: 0.7273 (mp0) REVERT: C 839 MET cc_start: 0.5618 (tpt) cc_final: 0.5166 (tpt) REVERT: D 358 MET cc_start: 0.8197 (mmm) cc_final: 0.7757 (mmm) REVERT: D 602 ILE cc_start: 0.7850 (pt) cc_final: 0.7615 (tp) REVERT: D 629 LYS cc_start: 0.8352 (tttt) cc_final: 0.7889 (tttt) REVERT: D 641 ILE cc_start: 0.8663 (tp) cc_final: 0.8358 (tp) REVERT: D 643 LEU cc_start: 0.8504 (tp) cc_final: 0.7946 (tt) REVERT: D 654 MET cc_start: 0.8607 (mmm) cc_final: 0.8400 (mmm) REVERT: D 739 MET cc_start: 0.8795 (mmm) cc_final: 0.8314 (mmm) outliers start: 1 outliers final: 0 residues processed: 376 average time/residue: 0.2802 time to fit residues: 180.0564 Evaluate side-chains 298 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 144 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 171 optimal weight: 0.0050 chunk 52 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 HIS A 801 HIS ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.136012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.118342 restraints weight = 63534.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.119476 restraints weight = 42086.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.120638 restraints weight = 32965.383| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23427 Z= 0.121 Angle : 0.635 15.309 32031 Z= 0.322 Chirality : 0.046 0.279 3832 Planarity : 0.005 0.084 4056 Dihedral : 6.357 59.513 3367 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.10 % Favored : 90.87 % Rotamer: Outliers : 0.04 % Allowed : 2.18 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.15), residues: 3122 helix: -0.66 (0.17), residues: 1032 sheet: -2.81 (0.28), residues: 307 loop : -2.59 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 166 HIS 0.015 0.001 HIS B 486 PHE 0.020 0.001 PHE A 775 TYR 0.028 0.001 TYR C 388 ARG 0.003 0.000 ARG C 411 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 2) link_NAG-ASN : angle 2.26853 ( 6) hydrogen bonds : bond 0.03677 ( 680) hydrogen bonds : angle 5.06792 ( 1881) SS BOND : bond 0.00280 ( 16) SS BOND : angle 1.35433 ( 32) covalent geometry : bond 0.00275 (23407) covalent geometry : angle 0.63304 (31993) Misc. bond : bond 0.00506 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 409 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 CYS cc_start: 0.6036 (t) cc_final: 0.5276 (t) REVERT: A 577 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7586 (tt0) REVERT: A 628 MET cc_start: 0.8300 (tmm) cc_final: 0.7649 (tmm) REVERT: B 307 MET cc_start: 0.5647 (mmt) cc_final: 0.5439 (mmt) REVERT: B 746 CYS cc_start: 0.6019 (m) cc_final: 0.5507 (m) REVERT: B 822 PHE cc_start: 0.6884 (m-80) cc_final: 0.6541 (m-80) REVERT: C 47 ASN cc_start: 0.8553 (m110) cc_final: 0.8074 (t0) REVERT: C 79 CYS cc_start: 0.5145 (p) cc_final: 0.4757 (p) REVERT: C 415 MET cc_start: 0.5180 (ttm) cc_final: 0.4729 (ttm) REVERT: C 457 CYS cc_start: 0.3872 (t) cc_final: 0.3148 (t) REVERT: C 491 MET cc_start: 0.7969 (mpp) cc_final: 0.7691 (mpp) REVERT: C 520 ASN cc_start: 0.8038 (p0) cc_final: 0.7574 (t0) REVERT: C 628 MET cc_start: 0.6557 (tmm) cc_final: 0.6035 (tmm) REVERT: C 662 MET cc_start: 0.9023 (tmm) cc_final: 0.8821 (tmm) REVERT: C 839 MET cc_start: 0.5973 (tpt) cc_final: 0.5339 (tpt) REVERT: D 497 MET cc_start: 0.8706 (mmp) cc_final: 0.7894 (mmp) REVERT: D 602 ILE cc_start: 0.7036 (pt) cc_final: 0.6626 (tt) REVERT: D 641 ILE cc_start: 0.8739 (tp) cc_final: 0.8493 (tp) REVERT: D 643 LEU cc_start: 0.8477 (tp) cc_final: 0.7891 (tt) REVERT: D 654 MET cc_start: 0.7889 (mmm) cc_final: 0.7677 (mmp) REVERT: D 739 MET cc_start: 0.8468 (mmm) cc_final: 0.7980 (mmm) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.2751 time to fit residues: 188.6958 Evaluate side-chains 317 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 57 optimal weight: 6.9990 chunk 81 optimal weight: 30.0000 chunk 269 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 280 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 730 HIS A 801 HIS ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN ** C 730 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.132915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.113806 restraints weight = 64301.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.115999 restraints weight = 47472.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.117035 restraints weight = 33386.262| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23427 Z= 0.180 Angle : 0.702 17.464 32031 Z= 0.355 Chirality : 0.047 0.253 3832 Planarity : 0.005 0.085 4056 Dihedral : 6.561 58.754 3367 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.33 % Favored : 87.64 % Rotamer: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.15), residues: 3122 helix: -0.65 (0.16), residues: 1026 sheet: -2.82 (0.27), residues: 299 loop : -2.65 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 166 HIS 0.019 0.002 HIS B 486 PHE 0.028 0.002 PHE D 169 TYR 0.025 0.002 TYR D 322 ARG 0.007 0.000 ARG D 693 Details of bonding type rmsd link_NAG-ASN : bond 0.00609 ( 2) link_NAG-ASN : angle 2.24467 ( 6) hydrogen bonds : bond 0.04034 ( 680) hydrogen bonds : angle 5.22389 ( 1881) SS BOND : bond 0.00343 ( 16) SS BOND : angle 1.32379 ( 32) covalent geometry : bond 0.00417 (23407) covalent geometry : angle 0.70017 (31993) Misc. bond : bond 0.00423 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6244 Ramachandran restraints generated. 3122 Oldfield, 0 Emsley, 3122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.8106 (ptm) cc_final: 0.7875 (ptt) REVERT: A 628 MET cc_start: 0.8281 (tmm) cc_final: 0.7778 (tmm) REVERT: B 307 MET cc_start: 0.5724 (mmt) cc_final: 0.5453 (mmt) REVERT: B 822 PHE cc_start: 0.7022 (m-80) cc_final: 0.6672 (m-80) REVERT: C 79 CYS cc_start: 0.5467 (p) cc_final: 0.5100 (p) REVERT: C 362 ASN cc_start: 0.8831 (p0) cc_final: 0.8580 (p0) REVERT: C 415 MET cc_start: 0.5216 (ttm) cc_final: 0.4793 (ttm) REVERT: C 457 CYS cc_start: 0.4109 (t) cc_final: 0.3427 (t) REVERT: C 628 MET cc_start: 0.6830 (tmm) cc_final: 0.6197 (tmm) REVERT: C 839 MET cc_start: 0.5970 (tpt) cc_final: 0.5397 (tpt) REVERT: D 602 ILE cc_start: 0.7160 (pt) cc_final: 0.6852 (tt) REVERT: D 629 LYS cc_start: 0.8436 (tttt) cc_final: 0.8106 (tttt) REVERT: D 643 LEU cc_start: 0.8502 (tp) cc_final: 0.8029 (tt) REVERT: D 739 MET cc_start: 0.8565 (mmm) cc_final: 0.8070 (mmm) outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.2991 time to fit residues: 192.8234 Evaluate side-chains 300 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.5489 > 50: distance: 17 - 23: 7.575 distance: 18 - 43: 27.141 distance: 23 - 24: 13.079 distance: 23 - 29: 8.918 distance: 24 - 25: 19.759 distance: 24 - 27: 17.041 distance: 25 - 26: 27.301 distance: 25 - 30: 10.429 distance: 26 - 54: 11.247 distance: 27 - 28: 20.905 distance: 28 - 29: 20.707 distance: 30 - 31: 10.855 distance: 31 - 32: 37.759 distance: 31 - 34: 28.440 distance: 32 - 33: 13.718 distance: 32 - 35: 20.305 distance: 35 - 36: 23.366 distance: 36 - 37: 8.472 distance: 36 - 39: 23.526 distance: 37 - 38: 17.426 distance: 37 - 43: 46.582 distance: 39 - 40: 31.717 distance: 40 - 41: 16.401 distance: 40 - 42: 15.999 distance: 43 - 44: 44.247 distance: 44 - 45: 42.370 distance: 44 - 47: 55.968 distance: 45 - 54: 37.221 distance: 47 - 48: 5.857 distance: 48 - 49: 27.881 distance: 49 - 50: 9.302 distance: 50 - 51: 17.718 distance: 51 - 52: 5.607 distance: 51 - 53: 8.783 distance: 54 - 55: 13.158 distance: 55 - 56: 23.707 distance: 55 - 58: 23.197 distance: 56 - 57: 34.434 distance: 56 - 62: 19.550 distance: 58 - 59: 17.627 distance: 59 - 60: 27.769 distance: 62 - 63: 31.076 distance: 62 - 68: 32.708 distance: 63 - 64: 38.673 distance: 63 - 66: 25.052 distance: 64 - 65: 13.094 distance: 64 - 69: 13.092 distance: 66 - 67: 9.518 distance: 67 - 68: 29.623 distance: 69 - 70: 27.470 distance: 70 - 71: 24.945 distance: 70 - 73: 33.474 distance: 71 - 72: 7.917 distance: 71 - 75: 58.270 distance: 73 - 74: 11.647 distance: 75 - 76: 28.905 distance: 76 - 77: 41.630 distance: 76 - 79: 20.718 distance: 77 - 78: 43.077 distance: 77 - 83: 22.821 distance: 79 - 80: 46.205 distance: 80 - 81: 11.353 distance: 80 - 82: 31.536 distance: 83 - 84: 39.176 distance: 84 - 85: 13.584 distance: 84 - 87: 20.469 distance: 85 - 86: 36.189 distance: 85 - 88: 28.192 distance: 88 - 89: 37.451 distance: 89 - 90: 37.438 distance: 89 - 92: 23.582 distance: 90 - 99: 33.983 distance: 92 - 93: 24.369 distance: 93 - 94: 18.749 distance: 93 - 95: 6.947 distance: 94 - 96: 11.821 distance: 95 - 97: 24.217 distance: 96 - 98: 30.171 distance: 97 - 98: 7.408