Starting phenix.real_space_refine on Tue Jun 24 06:43:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7te9_25843/06_2025/7te9_25843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7te9_25843/06_2025/7te9_25843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7te9_25843/06_2025/7te9_25843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7te9_25843/06_2025/7te9_25843.map" model { file = "/net/cci-nas-00/data/ceres_data/7te9_25843/06_2025/7te9_25843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7te9_25843/06_2025/7te9_25843.cif" } resolution = 3.92 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= 0.053 sd= 0.476 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 17983 2.51 5 N 4715 2.21 5 O 5270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28142 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6265 Classifications: {'peptide': 794} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 760} Chain breaks: 4 Chain: "B" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6084 Classifications: {'peptide': 784} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 26} Link IDs: {'PTRANS': 29, 'TRANS': 754} Chain breaks: 5 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 6265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6265 Classifications: {'peptide': 794} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 31, 'TRANS': 760} Chain breaks: 4 Chain: "D" Number of atoms: 6084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6084 Classifications: {'peptide': 784} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 26} Link IDs: {'PTRANS': 29, 'TRANS': 754} Chain breaks: 5 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 74 Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 899 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain breaks: 1 Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 16.60, per 1000 atoms: 0.59 Number of scatterers: 28142 At special positions: 0 Unit cell: (146.59, 223.31, 180.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 5270 8.00 N 4715 7.00 C 17983 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 329 " distance=2.04 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 475 " distance=2.04 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 476 " distance=2.03 Simple disulfide: pdb=" SG CYS A 765 " - pdb=" SG CYS A 819 " distance=2.04 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 476 " distance=2.03 Simple disulfide: pdb=" SG CYS C 765 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.04 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.80 Conformation dependent library (CDL) restraints added in 3.9 seconds 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6678 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 45 sheets defined 34.5% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.929A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 106 through 111 Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.418A pdb=" N TYR A 128 " --> pdb=" O MET A 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 4.157A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 183 Processing helix chain 'A' and resid 184 through 188 removed outlier: 3.819A pdb=" N ARG A 187 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 188 " --> pdb=" O GLU A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 184 through 188' Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.040A pdb=" N GLU A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 253 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.438A pdb=" N GLY A 265 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 266 " --> pdb=" O GLY A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 297 through 318 removed outlier: 3.713A pdb=" N HIS A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 318 " --> pdb=" O HIS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 520 through 528 removed outlier: 3.712A pdb=" N GLY A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 removed outlier: 3.792A pdb=" N GLN A 546 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR A 547 " --> pdb=" O ARG A 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 547' Processing helix chain 'A' and resid 585 through 604 Processing helix chain 'A' and resid 626 through 636 removed outlier: 3.809A pdb=" N GLY A 633 " --> pdb=" O TRP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 678 removed outlier: 3.503A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.553A pdb=" N ILE A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 726 Processing helix chain 'A' and resid 734 through 743 removed outlier: 3.838A pdb=" N ALA A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 764 removed outlier: 4.926A pdb=" N PHE A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 791 removed outlier: 4.369A pdb=" N GLN A 791 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 removed outlier: 3.773A pdb=" N ILE A 797 " --> pdb=" O VAL A 793 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 798 " --> pdb=" O SER A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 834 through 862 removed outlier: 4.454A pdb=" N LEU A 840 " --> pdb=" O GLY A 836 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL A 841 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 846 " --> pdb=" O ALA A 842 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE A 850 " --> pdb=" O VAL A 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.611A pdb=" N ILE B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.993A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 4.204A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 179 through 187 removed outlier: 3.645A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 220 through 223 removed outlier: 3.537A pdb=" N LEU B 223 " --> pdb=" O LEU B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.259A pdb=" N GLU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 312 Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.871A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.583A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.555A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.575A pdb=" N SER B 520 " --> pdb=" O ASN B 516 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 521' Processing helix chain 'B' and resid 557 through 567 removed outlier: 4.412A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.851A pdb=" N PHE B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 612 removed outlier: 3.669A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 654 removed outlier: 4.344A pdb=" N VAL B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 644 " --> pdb=" O VAL B 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 696 removed outlier: 3.690A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.725A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 740 Processing helix chain 'B' and resid 772 through 786 removed outlier: 3.501A pdb=" N VAL B 776 " --> pdb=" O TRP B 772 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 Processing helix chain 'B' and resid 793 through 796 Processing helix chain 'B' and resid 813 through 817 removed outlier: 3.989A pdb=" N ASP B 816 " --> pdb=" O LEU B 813 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 817 " --> pdb=" O ASP B 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 813 through 817' Processing helix chain 'B' and resid 818 through 838 removed outlier: 3.549A pdb=" N ALA B 827 " --> pdb=" O TYR B 823 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA B 828 " --> pdb=" O MET B 824 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 833 " --> pdb=" O MET B 829 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 841 No H-bonds generated for 'chain 'B' and resid 839 through 841' Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.930A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 106 through 111 Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.417A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 4.157A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 183 Processing helix chain 'C' and resid 184 through 188 removed outlier: 3.819A pdb=" N ARG C 187 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 188 " --> pdb=" O GLU C 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 184 through 188' Processing helix chain 'C' and resid 225 through 234 removed outlier: 4.040A pdb=" N GLU C 234 " --> pdb=" O MET C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 262 through 266 removed outlier: 4.437A pdb=" N GLY C 265 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 266 " --> pdb=" O GLY C 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 266' Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.712A pdb=" N HIS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP C 304 " --> pdb=" O ALA C 300 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 318 " --> pdb=" O HIS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 478 through 492 Processing helix chain 'C' and resid 520 through 528 removed outlier: 3.712A pdb=" N GLY C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 525 " --> pdb=" O GLY C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 removed outlier: 3.791A pdb=" N GLN C 546 " --> pdb=" O GLU C 543 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR C 547 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 543 through 547' Processing helix chain 'C' and resid 585 through 604 Processing helix chain 'C' and resid 626 through 636 removed outlier: 3.808A pdb=" N GLY C 633 " --> pdb=" O TRP C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 678 removed outlier: 3.504A pdb=" N ARG C 651 " --> pdb=" O SER C 647 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 653 " --> pdb=" O SER C 649 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 678 " --> pdb=" O ALA C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 717 removed outlier: 3.553A pdb=" N ILE C 712 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 717 " --> pdb=" O TYR C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 726 Processing helix chain 'C' and resid 734 through 743 removed outlier: 3.838A pdb=" N ALA C 738 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 764 removed outlier: 4.926A pdb=" N PHE C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 791 removed outlier: 4.369A pdb=" N GLN C 791 " --> pdb=" O PRO C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 803 removed outlier: 3.773A pdb=" N ILE C 797 " --> pdb=" O VAL C 793 " (cutoff:3.500A) removed outlier: 4.172A 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 862 removed outlier: 4.454A pdb=" N LEU C 840 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 841 " --> pdb=" O VAL C 837 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL C 846 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE C 849 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 850 " --> pdb=" O VAL C 846 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.611A pdb=" N ILE D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.993A pdb=" N ASP D 87 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 4.203A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 151 through 162 Processing helix chain 'D' and resid 179 through 187 removed outlier: 3.645A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN D 184 " --> pdb=" O GLN D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 220 through 223 removed outlier: 3.537A pdb=" N LEU D 223 " --> pdb=" O LEU D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 223' Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.259A pdb=" N GLU D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 312 Processing helix chain 'D' and resid 331 through 340 removed outlier: 3.872A pdb=" N ILE D 340 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 472 removed outlier: 3.582A pdb=" N LYS D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 removed outlier: 3.555A pdb=" N MET D 503 " --> pdb=" O GLY D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 521 removed outlier: 3.574A pdb=" N SER D 520 " --> pdb=" O ASN D 516 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 516 through 521' Processing helix chain 'D' and resid 557 through 567 removed outlier: 4.412A pdb=" N PHE D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL D 564 " --> pdb=" O VAL D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.851A pdb=" N PHE D 577 " --> pdb=" O ALA D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 603 through 612 removed outlier: 3.669A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY D 611 " --> pdb=" O TRP D 607 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 654 removed outlier: 4.344A pdb=" N VAL D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 641 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 644 " --> pdb=" O VAL D 640 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 696 removed outlier: 3.689A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 removed outlier: 3.724A pdb=" N HIS D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 740 Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.501A pdb=" N VAL D 776 " --> pdb=" O TRP D 772 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 778 " --> pdb=" O ARG D 774 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 792 Processing helix chain 'D' and resid 793 through 796 Processing helix chain 'D' and resid 813 through 817 removed outlier: 3.989A pdb=" N ASP D 816 " --> pdb=" O LEU D 813 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 817 " --> pdb=" O ASP D 814 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 813 through 817' Processing helix chain 'D' and resid 818 through 838 removed outlier: 3.549A pdb=" N ALA D 827 " --> pdb=" O TYR D 823 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA D 828 " --> pdb=" O MET D 824 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 833 " --> pdb=" O MET D 829 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE D 836 " --> pdb=" O SER D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 841 No H-bonds generated for 'chain 'D' and resid 839 through 841' Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.603A pdb=" N VAL A 27 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 11.670A pdb=" N ILE A 26 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 11.325A pdb=" N ALA A 89 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASN A 28 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU A 91 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY A 30 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 290 Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.693A pdb=" N THR A 423 " --> pdb=" O HIS A 498 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 533 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 433 through 434 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 511 removed outlier: 3.699A pdb=" N GLU A 509 " --> pdb=" O GLU A 518 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 518 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS A 516 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 750 through 753 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 73 removed outlier: 8.383A pdb=" N VAL B 71 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 39 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET B 73 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 41 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 203 through 204 removed outlier: 3.585A pdb=" N LEU B 203 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 228 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 278 through 281 removed outlier: 5.013A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 365 " --> pdb=" O SER B 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 378 through 380 Processing sheet with id=AB3, first strand: chain 'B' and resid 408 through 410 removed outlier: 6.195A pdb=" N ILE B 408 " --> pdb=" O TYR B 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 488 through 490 removed outlier: 3.968A pdb=" N LYS B 488 " --> pdb=" O ASN B 495 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 524 through 525 removed outlier: 4.116A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 766 " --> pdb=" O ASP B 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB8, first strand: chain 'B' and resid 534 through 538 removed outlier: 3.630A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.602A pdb=" N VAL C 27 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 11.671A pdb=" N ILE C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 11.323A pdb=" N ALA C 89 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN C 28 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AC2, first strand: chain 'C' and resid 288 through 290 Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 499 removed outlier: 3.694A pdb=" N THR C 423 " --> pdb=" O HIS C 498 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C 533 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 433 through 434 Processing sheet with id=AC5, first strand: chain 'C' and resid 508 through 511 removed outlier: 3.699A pdb=" N GLU C 509 " --> pdb=" O GLU C 518 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 518 " --> pdb=" O GLU C 509 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS C 516 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 750 through 753 Processing sheet with id=AC7, first strand: chain 'D' and resid 70 through 73 removed outlier: 8.383A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA D 38 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 123 " --> pdb=" O PHE D 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 203 through 204 removed outlier: 3.586A pdb=" N LEU D 203 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 228 " --> pdb=" O THR D 255 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 278 through 281 removed outlier: 5.014A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE D 365 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 378 through 380 Processing sheet with id=AD2, first strand: chain 'D' and resid 408 through 410 removed outlier: 6.195A pdb=" N ILE D 408 " --> pdb=" O TYR D 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD4, first strand: chain 'D' and resid 488 through 490 removed outlier: 3.967A pdb=" N LYS D 488 " --> pdb=" O ASN D 495 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 524 through 525 removed outlier: 4.115A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 766 " --> pdb=" O ASP D 524 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD7, first strand: chain 'D' and resid 534 through 538 removed outlier: 3.631A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.600A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS H 22 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.950A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.950A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.757A pdb=" N ALA L 13 " --> pdb=" O GLU L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AE4, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.573A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU M 81 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N CYS M 22 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU M 79 " --> pdb=" O CYS M 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 45 through 47 removed outlier: 3.813A pdb=" N SER M 35 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA M 97 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET M 93 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.758A pdb=" N ALA N 13 " --> pdb=" O GLU N 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AE9, first strand: chain 'N' and resid 45 through 46 852 hydrogen bonds defined for protein. 2424 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: 11.69 Time building geometry restraints manager: 8.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6032 1.33 - 1.45: 6757 1.45 - 1.57: 15665 1.57 - 1.70: 2 1.70 - 1.82: 298 Bond restraints: 28754 Sorted by residual: bond pdb=" C SER D 63 " pdb=" N VAL D 64 " ideal model delta sigma weight residual 1.330 1.204 0.126 1.57e-02 4.06e+03 6.42e+01 bond pdb=" CA THR A 830 " pdb=" CB THR A 830 " ideal model delta sigma weight residual 1.530 1.573 -0.043 1.69e-02 3.50e+03 6.51e+00 bond pdb=" CA THR C 830 " pdb=" CB THR C 830 " ideal model delta sigma weight residual 1.530 1.573 -0.043 1.69e-02 3.50e+03 6.51e+00 bond pdb=" CB THR A 830 " pdb=" CG2 THR A 830 " ideal model delta sigma weight residual 1.521 1.601 -0.080 3.30e-02 9.18e+02 5.85e+00 bond pdb=" CB THR C 830 " pdb=" CG2 THR C 830 " ideal model delta sigma weight residual 1.521 1.600 -0.079 3.30e-02 9.18e+02 5.74e+00 ... (remaining 28749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.08: 38751 5.08 - 10.16: 179 10.16 - 15.25: 6 15.25 - 20.33: 2 20.33 - 25.41: 4 Bond angle restraints: 38942 Sorted by residual: angle pdb=" O SER D 63 " pdb=" C SER D 63 " pdb=" N VAL D 64 " ideal model delta sigma weight residual 122.23 97.18 25.05 1.30e+00 5.92e-01 3.71e+02 angle pdb=" O SER B 63 " pdb=" C SER B 63 " pdb=" N VAL B 64 " ideal model delta sigma weight residual 122.33 96.92 25.41 1.34e+00 5.57e-01 3.60e+02 angle pdb=" CA SER B 63 " pdb=" C SER B 63 " pdb=" N VAL B 64 " ideal model delta sigma weight residual 117.82 142.20 -24.38 1.42e+00 4.96e-01 2.95e+02 angle pdb=" CA SER D 63 " pdb=" C SER D 63 " pdb=" N VAL D 64 " ideal model delta sigma weight residual 117.48 140.42 -22.94 1.41e+00 5.03e-01 2.65e+02 angle pdb=" C SER B 63 " pdb=" N VAL B 64 " pdb=" CA VAL B 64 " ideal model delta sigma weight residual 122.67 140.41 -17.74 1.68e+00 3.54e-01 1.11e+02 ... (remaining 38937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15096 17.92 - 35.84: 1679 35.84 - 53.76: 285 53.76 - 71.69: 97 71.69 - 89.61: 17 Dihedral angle restraints: 17174 sinusoidal: 6779 harmonic: 10395 Sorted by residual: dihedral pdb=" CA PHE A 113 " pdb=" C PHE A 113 " pdb=" N TYR A 114 " pdb=" CA TYR A 114 " ideal model delta harmonic sigma weight residual 180.00 103.89 76.11 0 5.00e+00 4.00e-02 2.32e+02 dihedral pdb=" CA PHE C 113 " pdb=" C PHE C 113 " pdb=" N TYR C 114 " pdb=" CA TYR C 114 " ideal model delta harmonic sigma weight residual 180.00 103.92 76.08 0 5.00e+00 4.00e-02 2.32e+02 dihedral pdb=" CA LEU D 367 " pdb=" C LEU D 367 " pdb=" N ASN D 368 " pdb=" CA ASN D 368 " ideal model delta harmonic sigma weight residual 180.00 116.08 63.92 0 5.00e+00 4.00e-02 1.63e+02 ... (remaining 17171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3301 0.060 - 0.120: 845 0.120 - 0.180: 174 0.180 - 0.240: 31 0.240 - 0.300: 4 Chirality restraints: 4355 Sorted by residual: chirality pdb=" CB ILE A 26 " pdb=" CA ILE A 26 " pdb=" CG1 ILE A 26 " pdb=" CG2 ILE A 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C 26 " pdb=" CA ILE C 26 " pdb=" CG1 ILE C 26 " pdb=" CG2 ILE C 26 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE D 630 " pdb=" CA ILE D 630 " pdb=" CG1 ILE D 630 " pdb=" CG2 ILE D 630 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4352 not shown) Planarity restraints: 4945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 63 " 0.035 2.00e-02 2.50e+03 5.81e-02 3.37e+01 pdb=" C SER D 63 " -0.100 2.00e-02 2.50e+03 pdb=" O SER D 63 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL D 64 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 63 " -0.027 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C SER B 63 " 0.076 2.00e-02 2.50e+03 pdb=" O SER B 63 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL B 64 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 567 " 0.059 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO C 568 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO C 568 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 568 " 0.049 5.00e-02 4.00e+02 ... (remaining 4942 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.72: 2 1.72 - 2.52: 226 2.52 - 3.31: 31858 3.31 - 4.11: 66036 4.11 - 4.90: 115199 Warning: very small nonbonded interaction distances. Nonbonded interactions: 213321 Sorted by model distance: nonbonded pdb=" O PHE H 109 " pdb=" OH TYR L 36 " model vdw 0.928 3.040 nonbonded pdb=" O PHE M 109 " pdb=" OH TYR N 36 " model vdw 1.072 3.040 nonbonded pdb=" OD2 ASP B 58 " pdb=" OG SER M 52 " model vdw 1.782 3.040 nonbonded pdb=" OH TYR H 108 " pdb=" O ILE L 33 " model vdw 1.896 3.040 nonbonded pdb=" OH TYR H 108 " pdb=" C ILE L 33 " model vdw 1.922 3.270 ... (remaining 213316 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = (chain 'H' and resid 2 through 120) selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 1.650 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: 0.040 Extract box with map and model: 1.110 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 65.770 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.210 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:3.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.006 0.126 28774 Z= 0.283 Angle : 1.063 25.410 38982 Z= 0.622 Chirality : 0.057 0.300 4355 Planarity : 0.008 0.090 4945 Dihedral : 15.479 89.606 10436 Min Nonbonded Distance : 0.928 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.62 % Allowed : 9.79 % Favored : 89.59 % Rotamer: Outliers : 1.21 % Allowed : 7.88 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 9.86 % Twisted General : 1.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.11), residues: 3545 helix: -3.17 (0.10), residues: 1128 sheet: -1.85 (0.22), residues: 498 loop : -3.16 (0.12), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 796 HIS 0.011 0.001 HIS L 38 PHE 0.025 0.002 PHE D 529 TYR 0.034 0.003 TYR N 87 ARG 0.009 0.001 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.19741 ( 847) hydrogen bonds : angle 8.08523 ( 2424) SS BOND : bond 0.00730 ( 20) SS BOND : angle 1.99313 ( 40) covalent geometry : bond 0.00581 (28754) covalent geometry : angle 1.06137 (38942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 3.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.9089 (mtm) cc_final: 0.8836 (mtt) REVERT: A 783 MET cc_start: 0.6818 (mtp) cc_final: 0.6522 (mtp) REVERT: A 819 CYS cc_start: 0.7135 (OUTLIER) cc_final: 0.6324 (p) REVERT: A 834 MET cc_start: 0.7257 (mpp) cc_final: 0.6305 (mpp) REVERT: B 561 MET cc_start: 0.8882 (mmt) cc_final: 0.8411 (ttp) REVERT: B 824 MET cc_start: 0.7198 (mmt) cc_final: 0.6700 (mmm) REVERT: C 347 MET cc_start: 0.9049 (ptp) cc_final: 0.8709 (ptm) REVERT: C 819 CYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6063 (p) REVERT: C 839 MET cc_start: 0.8446 (ptm) cc_final: 0.8244 (ppp) REVERT: D 824 MET cc_start: 0.6981 (mmt) cc_final: 0.6704 (mmm) REVERT: H 37 VAL cc_start: 0.1189 (OUTLIER) cc_final: 0.0441 (p) REVERT: H 110 ASP cc_start: 0.8926 (p0) cc_final: 0.8098 (t0) REVERT: L 61 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7820 (mtm180) REVERT: L 82 ASP cc_start: 0.1948 (m-30) cc_final: 0.1677 (m-30) REVERT: M 34 MET cc_start: 0.7628 (mmm) cc_final: 0.7400 (mmm) REVERT: N 4 MET cc_start: 0.4121 (tmm) cc_final: 0.3696 (tmm) REVERT: N 92 ASP cc_start: 0.4220 (OUTLIER) cc_final: 0.3818 (p0) outliers start: 37 outliers final: 7 residues processed: 268 average time/residue: 0.4638 time to fit residues: 198.0786 Evaluate side-chains 187 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain N residue 92 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 182 optimal weight: 8.9990 chunk 144 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 508 GLN A 817 GLN B 95 GLN B 359 HIS B 385 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 ASN B 697 ASN B 767 GLN C 224 ASN C 508 GLN C 817 GLN D 95 GLN D 359 HIS D 385 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN D 697 ASN D 767 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.048623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.036253 restraints weight = 306602.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.036204 restraints weight = 177760.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.036611 restraints weight = 119868.722| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28774 Z= 0.240 Angle : 0.795 9.494 38982 Z= 0.420 Chirality : 0.046 0.221 4355 Planarity : 0.006 0.092 4945 Dihedral : 8.499 76.564 3883 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.42 % Favored : 90.13 % Rotamer: Outliers : 1.83 % Allowed : 11.58 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 9.86 % Twisted General : 0.90 % 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: -3.35 (0.12), residues: 3545 helix: -1.40 (0.14), residues: 1224 sheet: -1.70 (0.22), residues: 511 loop : -3.05 (0.12), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 796 HIS 0.006 0.001 HIS B 54 PHE 0.024 0.002 PHE B 563 TYR 0.022 0.002 TYR B 167 ARG 0.007 0.001 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.04516 ( 847) hydrogen bonds : angle 5.80317 ( 2424) SS BOND : bond 0.00436 ( 20) SS BOND : angle 1.66618 ( 40) covalent geometry : bond 0.00500 (28754) covalent geometry : angle 0.79317 (38942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8073 (ttt) cc_final: 0.7706 (ttt) REVERT: A 131 LYS cc_start: 0.8207 (mmtm) cc_final: 0.7529 (tppt) REVERT: A 533 MET cc_start: 0.8896 (mmm) cc_final: 0.8484 (tpt) REVERT: A 819 CYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7006 (p) REVERT: B 508 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8618 (mmm) REVERT: B 537 MET cc_start: 0.8916 (tmm) cc_final: 0.8592 (tmm) REVERT: C 125 MET cc_start: 0.8162 (ttt) cc_final: 0.7944 (ttt) REVERT: C 131 LYS cc_start: 0.8405 (mmtm) cc_final: 0.7808 (tppt) REVERT: C 533 MET cc_start: 0.8596 (mmm) cc_final: 0.8062 (mmm) REVERT: C 597 MET cc_start: 0.9624 (mmm) cc_final: 0.9243 (mtp) REVERT: C 819 CYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7418 (p) REVERT: C 839 MET cc_start: 0.8648 (ptm) cc_final: 0.8292 (ppp) REVERT: D 73 MET cc_start: 0.8949 (tpp) cc_final: 0.8660 (mmm) REVERT: D 508 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8693 (mmm) REVERT: D 537 MET cc_start: 0.8869 (tmm) cc_final: 0.8560 (tmm) REVERT: H 83 MET cc_start: 0.3811 (mmt) cc_final: 0.3542 (mmt) REVERT: L 82 ASP cc_start: 0.4776 (m-30) cc_final: 0.4488 (m-30) REVERT: M 83 MET cc_start: 0.3180 (mmt) cc_final: 0.2927 (mmt) REVERT: N 4 MET cc_start: 0.6442 (tmm) cc_final: 0.5867 (tmm) outliers start: 56 outliers final: 23 residues processed: 226 average time/residue: 0.3714 time to fit residues: 137.8360 Evaluate side-chains 197 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 819 CYS Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 796 TRP Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain N residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 155 optimal weight: 6.9990 chunk 347 optimal weight: 50.0000 chunk 106 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 330 optimal weight: 0.5980 chunk 332 optimal weight: 40.0000 chunk 256 optimal weight: 8.9990 chunk 318 optimal weight: 20.0000 chunk 247 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN B 218 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN H 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.047959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.034386 restraints weight = 310303.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.034509 restraints weight = 181893.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.034817 restraints weight = 129574.768| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 28774 Z= 0.224 Angle : 0.751 14.597 38982 Z= 0.394 Chirality : 0.045 0.186 4355 Planarity : 0.005 0.091 4945 Dihedral : 7.984 75.673 3879 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.16 % Favored : 89.45 % Rotamer: Outliers : 2.36 % Allowed : 12.99 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.70 % 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: -2.75 (0.13), residues: 3545 helix: -0.48 (0.15), residues: 1200 sheet: -1.76 (0.21), residues: 547 loop : -2.87 (0.13), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 796 HIS 0.007 0.001 HIS D 359 PHE 0.014 0.002 PHE A 805 TYR 0.023 0.002 TYR B 167 ARG 0.010 0.001 ARG M 44 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 847) hydrogen bonds : angle 5.37193 ( 2424) SS BOND : bond 0.00761 ( 20) SS BOND : angle 1.72827 ( 40) covalent geometry : bond 0.00471 (28754) covalent geometry : angle 0.74919 (38942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 174 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.8053 (ttt) cc_final: 0.7714 (ttt) REVERT: A 131 LYS cc_start: 0.8155 (mmtm) cc_final: 0.7547 (tppt) REVERT: A 154 MET cc_start: 0.9263 (mtm) cc_final: 0.9007 (mtm) REVERT: A 230 MET cc_start: 0.9237 (mtm) cc_final: 0.8931 (mtt) REVERT: A 533 MET cc_start: 0.9196 (mmm) cc_final: 0.8766 (tpp) REVERT: B 134 MET cc_start: 0.8267 (tmm) cc_final: 0.8034 (ppp) REVERT: B 537 MET cc_start: 0.8809 (tmm) cc_final: 0.8419 (tmm) REVERT: C 125 MET cc_start: 0.8144 (ttt) cc_final: 0.7937 (ttt) REVERT: C 131 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7641 (tppt) REVERT: C 154 MET cc_start: 0.9293 (mtm) cc_final: 0.9041 (mtm) REVERT: C 533 MET cc_start: 0.9166 (mmm) cc_final: 0.8828 (mmm) REVERT: C 597 MET cc_start: 0.9655 (mmm) cc_final: 0.9332 (mtm) REVERT: C 839 MET cc_start: 0.8607 (ptm) cc_final: 0.8131 (ppp) REVERT: D 307 MET cc_start: 0.8652 (tpt) cc_final: 0.8167 (tmm) REVERT: D 430 MET cc_start: 0.8575 (tmm) cc_final: 0.7727 (tmm) REVERT: D 508 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8535 (mmm) REVERT: D 537 MET cc_start: 0.8862 (tmm) cc_final: 0.8516 (tmm) REVERT: D 561 MET cc_start: 0.9264 (ptp) cc_final: 0.9059 (ptp) REVERT: D 565 MET cc_start: 0.8619 (mmt) cc_final: 0.8342 (mpp) REVERT: D 739 MET cc_start: 0.9308 (mmm) cc_final: 0.9035 (mmm) REVERT: D 767 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.5708 (mp10) REVERT: L 85 THR cc_start: 0.6119 (OUTLIER) cc_final: 0.5872 (t) REVERT: M 83 MET cc_start: 0.2741 (mmt) cc_final: 0.2365 (mmt) outliers start: 72 outliers final: 35 residues processed: 232 average time/residue: 0.3772 time to fit residues: 143.3580 Evaluate side-chains 201 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 834 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 796 TRP Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain L residue 30 ASN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 256 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 299 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 123 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 311 optimal weight: 0.0040 chunk 172 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN H 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.048121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.035316 restraints weight = 311416.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.035263 restraints weight = 179973.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.035694 restraints weight = 124502.984| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28774 Z= 0.171 Angle : 0.722 14.833 38982 Z= 0.373 Chirality : 0.045 0.180 4355 Planarity : 0.005 0.089 4945 Dihedral : 7.609 74.380 3877 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.24 % Favored : 89.37 % Rotamer: Outliers : 2.13 % Allowed : 15.11 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.61 % 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: -2.43 (0.14), residues: 3545 helix: -0.12 (0.15), residues: 1208 sheet: -1.73 (0.21), residues: 561 loop : -2.72 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 796 HIS 0.005 0.001 HIS L 38 PHE 0.020 0.001 PHE H 109 TYR 0.020 0.002 TYR A 253 ARG 0.009 0.000 ARG N 69 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 847) hydrogen bonds : angle 5.10442 ( 2424) SS BOND : bond 0.00484 ( 20) SS BOND : angle 2.14030 ( 40) covalent geometry : bond 0.00366 (28754) covalent geometry : angle 0.71899 (38942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 173 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9324 (mtt) cc_final: 0.8665 (mmm) REVERT: A 125 MET cc_start: 0.8068 (ttt) cc_final: 0.7681 (ttt) REVERT: A 131 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7529 (tppt) REVERT: A 154 MET cc_start: 0.9264 (mtm) cc_final: 0.8857 (mtm) REVERT: A 230 MET cc_start: 0.9233 (mtm) cc_final: 0.8905 (mtt) REVERT: A 583 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7116 (mt) REVERT: B 134 MET cc_start: 0.8280 (tmm) cc_final: 0.8076 (ppp) REVERT: B 537 MET cc_start: 0.8801 (tmm) cc_final: 0.8364 (tmm) REVERT: C 74 MET cc_start: 0.9279 (mtt) cc_final: 0.8585 (mmm) REVERT: C 125 MET cc_start: 0.8163 (ttt) cc_final: 0.7840 (ttt) REVERT: C 131 LYS cc_start: 0.8281 (mmtm) cc_final: 0.7765 (tppt) REVERT: C 583 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7023 (mt) REVERT: C 597 MET cc_start: 0.9628 (mmm) cc_final: 0.9381 (mtm) REVERT: C 839 MET cc_start: 0.8518 (ptm) cc_final: 0.8046 (ppp) REVERT: D 142 MET cc_start: 0.8908 (mtp) cc_final: 0.8693 (mtm) REVERT: D 430 MET cc_start: 0.8587 (tmm) cc_final: 0.7734 (tmm) REVERT: D 508 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8421 (mmp) REVERT: D 537 MET cc_start: 0.8851 (tmm) cc_final: 0.8456 (tmm) REVERT: D 565 MET cc_start: 0.8794 (mmt) cc_final: 0.8563 (mmm) REVERT: D 739 MET cc_start: 0.9294 (mmm) cc_final: 0.8990 (mmm) REVERT: D 767 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.5885 (mp10) REVERT: M 20 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.4239 (pp) REVERT: M 83 MET cc_start: 0.3575 (mmt) cc_final: 0.0918 (ptp) REVERT: M 118 VAL cc_start: 0.6674 (OUTLIER) cc_final: 0.5747 (m) outliers start: 65 outliers final: 36 residues processed: 229 average time/residue: 0.3923 time to fit residues: 145.3571 Evaluate side-chains 208 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 486 HIS Chi-restraints excluded: chain D residue 508 MET Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 796 TRP Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 145 optimal weight: 0.9980 chunk 15 optimal weight: 0.0870 chunk 352 optimal weight: 50.0000 chunk 331 optimal weight: 50.0000 chunk 355 optimal weight: 3.9990 chunk 343 optimal weight: 0.2980 chunk 237 optimal weight: 10.0000 chunk 102 optimal weight: 0.0970 chunk 224 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 319 optimal weight: 50.0000 overall best weight: 1.0958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 HIS H 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.048940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.034878 restraints weight = 304095.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.035670 restraints weight = 177948.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.036126 restraints weight = 129533.436| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28774 Z= 0.115 Angle : 0.692 24.540 38982 Z= 0.352 Chirality : 0.044 0.177 4355 Planarity : 0.005 0.084 4945 Dihedral : 7.199 71.703 3876 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.65 % Favored : 89.96 % Rotamer: Outliers : 1.93 % Allowed : 16.36 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 7.75 % Twisted General : 0.52 % 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: -2.15 (0.14), residues: 3545 helix: 0.14 (0.15), residues: 1210 sheet: -1.54 (0.21), residues: 557 loop : -2.59 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 796 HIS 0.010 0.001 HIS B 703 PHE 0.014 0.001 PHE A 113 TYR 0.020 0.001 TYR A 253 ARG 0.015 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 847) hydrogen bonds : angle 4.87264 ( 2424) SS BOND : bond 0.00325 ( 20) SS BOND : angle 1.94114 ( 40) covalent geometry : bond 0.00251 (28754) covalent geometry : angle 0.68921 (38942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9365 (mtt) cc_final: 0.8725 (mmm) REVERT: A 125 MET cc_start: 0.7962 (ttt) cc_final: 0.7644 (ttt) REVERT: A 131 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7672 (tppt) REVERT: A 230 MET cc_start: 0.9255 (mtm) cc_final: 0.8929 (mtt) REVERT: A 583 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7118 (mt) REVERT: B 497 MET cc_start: 0.8886 (mmt) cc_final: 0.8641 (mmt) REVERT: B 537 MET cc_start: 0.8803 (tmm) cc_final: 0.8353 (tmm) REVERT: C 74 MET cc_start: 0.9315 (mtt) cc_final: 0.8660 (mmm) REVERT: C 125 MET cc_start: 0.8156 (ttt) cc_final: 0.7832 (ttt) REVERT: C 154 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.8529 (mtm) REVERT: C 230 MET cc_start: 0.9179 (mtp) cc_final: 0.8733 (mpp) REVERT: C 375 MET cc_start: 0.8822 (mmm) cc_final: 0.8076 (mmp) REVERT: C 583 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7068 (mt) REVERT: C 597 MET cc_start: 0.9664 (mmm) cc_final: 0.9409 (mtt) REVERT: C 727 MET cc_start: 0.8241 (mmm) cc_final: 0.8023 (mmm) REVERT: D 142 MET cc_start: 0.9000 (mtp) cc_final: 0.8752 (mtm) REVERT: D 430 MET cc_start: 0.8416 (tmm) cc_final: 0.7569 (tmm) REVERT: D 537 MET cc_start: 0.8822 (tmm) cc_final: 0.8379 (tmm) REVERT: D 565 MET cc_start: 0.8787 (mmt) cc_final: 0.8549 (mmm) REVERT: D 739 MET cc_start: 0.9306 (mmm) cc_final: 0.8968 (mmm) REVERT: M 20 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.4340 (pp) REVERT: M 83 MET cc_start: 0.3797 (mmt) cc_final: 0.2181 (ptp) REVERT: M 118 VAL cc_start: 0.6340 (OUTLIER) cc_final: 0.5540 (m) outliers start: 59 outliers final: 35 residues processed: 220 average time/residue: 0.3847 time to fit residues: 139.8797 Evaluate side-chains 206 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 89 MET Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 796 TRP Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 131 optimal weight: 0.7980 chunk 296 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 172 optimal weight: 0.0470 chunk 269 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 324 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.048295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.034379 restraints weight = 311504.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.035048 restraints weight = 184448.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.035420 restraints weight = 132995.448| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28774 Z= 0.140 Angle : 0.696 19.810 38982 Z= 0.353 Chirality : 0.044 0.205 4355 Planarity : 0.004 0.082 4945 Dihedral : 6.985 71.231 3873 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.01 % Favored : 89.65 % Rotamer: Outliers : 2.19 % Allowed : 17.01 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % 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: -2.00 (0.14), residues: 3545 helix: 0.33 (0.16), residues: 1216 sheet: -1.60 (0.21), residues: 571 loop : -2.51 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 796 HIS 0.004 0.001 HIS L 38 PHE 0.017 0.001 PHE L 97 TYR 0.020 0.001 TYR A 253 ARG 0.004 0.000 ARG N 69 Details of bonding type rmsd hydrogen bonds : bond 0.03235 ( 847) hydrogen bonds : angle 4.82587 ( 2424) SS BOND : bond 0.00324 ( 20) SS BOND : angle 1.77409 ( 40) covalent geometry : bond 0.00304 (28754) covalent geometry : angle 0.69451 (38942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 169 time to evaluate : 3.274 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 74 MET cc_start: 0.9399 (mtt) cc_final: 0.8859 (mmm) REVERT: A 125 MET cc_start: 0.7959 (ttt) cc_final: 0.7629 (ttt) REVERT: A 131 LYS cc_start: 0.7850 (mmtm) cc_final: 0.7618 (tppt) REVERT: A 154 MET cc_start: 0.9318 (mtm) cc_final: 0.8872 (mtm) REVERT: A 230 MET cc_start: 0.9263 (mtm) cc_final: 0.8934 (mtt) REVERT: A 375 MET cc_start: 0.8748 (mmm) cc_final: 0.8023 (mmp) REVERT: A 583 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7227 (mt) REVERT: A 839 MET cc_start: 0.8882 (ttt) cc_final: 0.8501 (ppp) REVERT: B 142 MET cc_start: 0.9040 (mtp) cc_final: 0.7657 (ptp) REVERT: B 474 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: B 497 MET cc_start: 0.8982 (mmt) cc_final: 0.8694 (mmt) REVERT: B 530 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8916 (mm) REVERT: B 537 MET cc_start: 0.8846 (tmm) cc_final: 0.8417 (tmm) REVERT: B 797 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7915 (mm) REVERT: C 74 MET cc_start: 0.9364 (mtt) cc_final: 0.8696 (mmm) REVERT: C 125 MET cc_start: 0.8168 (ttt) cc_final: 0.7788 (ttt) REVERT: C 154 MET cc_start: 0.9344 (OUTLIER) cc_final: 0.8544 (mtm) REVERT: C 230 MET cc_start: 0.9187 (mtp) cc_final: 0.8729 (mpp) REVERT: C 375 MET cc_start: 0.8860 (mmm) cc_final: 0.8313 (mmp) REVERT: C 583 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7178 (mt) REVERT: C 597 MET cc_start: 0.9645 (mmm) cc_final: 0.9390 (mtt) REVERT: C 727 MET cc_start: 0.8364 (mmm) cc_final: 0.8134 (mmm) REVERT: D 430 MET cc_start: 0.8552 (tmm) cc_final: 0.7614 (tmm) REVERT: D 537 MET cc_start: 0.8831 (tmm) cc_final: 0.8407 (tmm) REVERT: D 565 MET cc_start: 0.8909 (mmt) cc_final: 0.8640 (mmm) REVERT: D 739 MET cc_start: 0.9277 (mmm) cc_final: 0.8961 (mmm) REVERT: L 47 LEU cc_start: 0.3527 (OUTLIER) cc_final: 0.2601 (mm) REVERT: M 20 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.4544 (pp) REVERT: M 83 MET cc_start: 0.3554 (mmt) cc_final: 0.1590 (ptp) REVERT: M 118 VAL cc_start: 0.6226 (OUTLIER) cc_final: 0.5297 (m) REVERT: N 79 GLU cc_start: 0.4971 (mm-30) cc_final: 0.4488 (pm20) outliers start: 67 outliers final: 43 residues processed: 230 average time/residue: 0.3716 time to fit residues: 141.3695 Evaluate side-chains 213 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 109 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 343 optimal weight: 50.0000 chunk 70 optimal weight: 0.3980 chunk 175 optimal weight: 0.9990 chunk 280 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN D 218 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 GLN D 767 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.047551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.035321 restraints weight = 311376.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.035024 restraints weight = 185770.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.035474 restraints weight = 127738.726| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28774 Z= 0.195 Angle : 0.735 17.584 38982 Z= 0.373 Chirality : 0.044 0.274 4355 Planarity : 0.005 0.082 4945 Dihedral : 7.032 71.953 3873 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.10 % Favored : 89.56 % Rotamer: Outliers : 2.16 % Allowed : 17.44 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3545 helix: 0.36 (0.16), residues: 1220 sheet: -1.61 (0.21), residues: 577 loop : -2.49 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 796 HIS 0.005 0.001 HIS L 49 PHE 0.012 0.001 PHE A 113 TYR 0.021 0.002 TYR B 167 ARG 0.010 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 847) hydrogen bonds : angle 4.93919 ( 2424) SS BOND : bond 0.00379 ( 20) SS BOND : angle 1.67218 ( 40) covalent geometry : bond 0.00419 (28754) covalent geometry : angle 0.73350 (38942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 164 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9420 (mtt) cc_final: 0.8899 (mmm) REVERT: A 125 MET cc_start: 0.7995 (ttt) cc_final: 0.7554 (ttt) REVERT: A 131 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7580 (tppt) REVERT: A 230 MET cc_start: 0.9247 (mtm) cc_final: 0.8914 (mtt) REVERT: A 583 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7249 (mt) REVERT: B 474 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: B 537 MET cc_start: 0.8822 (tmm) cc_final: 0.8436 (tmm) REVERT: B 739 MET cc_start: 0.9294 (mmm) cc_final: 0.9050 (mmm) REVERT: B 797 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7894 (mm) REVERT: C 39 GLU cc_start: 0.9514 (OUTLIER) cc_final: 0.9311 (mp0) REVERT: C 74 MET cc_start: 0.9420 (mtt) cc_final: 0.8914 (mmm) REVERT: C 125 MET cc_start: 0.8133 (ttt) cc_final: 0.7754 (ttt) REVERT: C 154 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8561 (mtm) REVERT: C 583 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7193 (mt) REVERT: C 597 MET cc_start: 0.9635 (mmm) cc_final: 0.9393 (mtt) REVERT: C 727 MET cc_start: 0.8461 (mmm) cc_final: 0.8177 (mmm) REVERT: D 430 MET cc_start: 0.8632 (tmm) cc_final: 0.7653 (tmm) REVERT: D 474 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: D 537 MET cc_start: 0.8825 (tmm) cc_final: 0.8440 (tmm) REVERT: D 561 MET cc_start: 0.9343 (ptp) cc_final: 0.8949 (ptp) REVERT: D 767 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6489 (mp10) REVERT: M 20 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.3871 (pp) REVERT: M 83 MET cc_start: 0.3846 (mmt) cc_final: 0.2332 (ptp) REVERT: M 118 VAL cc_start: 0.6195 (OUTLIER) cc_final: 0.5183 (m) REVERT: N 61 ARG cc_start: 0.2781 (ptt90) cc_final: 0.2382 (ptt-90) outliers start: 66 outliers final: 43 residues processed: 226 average time/residue: 0.3848 time to fit residues: 144.0939 Evaluate side-chains 212 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 474 PHE Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 45 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 114 optimal weight: 10.0000 chunk 320 optimal weight: 40.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.047013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.2990 r_free = 0.2990 target = 0.032916 restraints weight = 314504.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.033622 restraints weight = 185196.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.033977 restraints weight = 135177.731| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28774 Z= 0.220 Angle : 0.774 12.962 38982 Z= 0.391 Chirality : 0.045 0.264 4355 Planarity : 0.005 0.083 4945 Dihedral : 7.128 72.459 3873 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.63 % Favored : 89.03 % Rotamer: Outliers : 2.49 % Allowed : 17.99 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.14), residues: 3545 helix: 0.38 (0.15), residues: 1214 sheet: -1.70 (0.21), residues: 605 loop : -2.47 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 796 HIS 0.005 0.001 HIS D 359 PHE 0.014 0.001 PHE D 563 TYR 0.023 0.002 TYR B 167 ARG 0.004 0.000 ARG C 784 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 847) hydrogen bonds : angle 5.05287 ( 2424) SS BOND : bond 0.00853 ( 20) SS BOND : angle 2.03655 ( 40) covalent geometry : bond 0.00469 (28754) covalent geometry : angle 0.77197 (38942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 166 time to evaluate : 3.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9421 (mtt) cc_final: 0.8893 (mmm) REVERT: A 125 MET cc_start: 0.8004 (ttt) cc_final: 0.7591 (ttt) REVERT: A 131 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7635 (tppt) REVERT: A 154 MET cc_start: 0.9307 (mtm) cc_final: 0.8803 (mtm) REVERT: A 230 MET cc_start: 0.9222 (mtm) cc_final: 0.8908 (mtt) REVERT: A 375 MET cc_start: 0.8754 (mmm) cc_final: 0.8016 (mmp) REVERT: A 583 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7248 (mt) REVERT: B 142 MET cc_start: 0.9040 (mtp) cc_final: 0.7711 (ptp) REVERT: B 537 MET cc_start: 0.8761 (tmm) cc_final: 0.8411 (tmm) REVERT: B 739 MET cc_start: 0.9268 (mmm) cc_final: 0.9003 (mmm) REVERT: B 797 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8205 (mm) REVERT: C 74 MET cc_start: 0.9444 (mtt) cc_final: 0.8952 (mmm) REVERT: C 125 MET cc_start: 0.8133 (ttt) cc_final: 0.7779 (ttt) REVERT: C 154 MET cc_start: 0.9289 (OUTLIER) cc_final: 0.8498 (mtm) REVERT: C 230 MET cc_start: 0.9242 (mtp) cc_final: 0.8929 (ptp) REVERT: C 375 MET cc_start: 0.8859 (mmm) cc_final: 0.8124 (mmp) REVERT: C 583 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7203 (mt) REVERT: C 597 MET cc_start: 0.9651 (mmm) cc_final: 0.9415 (mtt) REVERT: C 727 MET cc_start: 0.8587 (mmm) cc_final: 0.8294 (mmm) REVERT: C 781 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9238 (mm) REVERT: C 783 MET cc_start: 0.8183 (tpp) cc_final: 0.7962 (tpp) REVERT: D 430 MET cc_start: 0.8673 (tmm) cc_final: 0.7688 (tmm) REVERT: D 537 MET cc_start: 0.8797 (tmm) cc_final: 0.8434 (tmm) REVERT: D 739 MET cc_start: 0.9169 (mmm) cc_final: 0.8933 (mmm) REVERT: D 767 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6131 (mp10) REVERT: M 20 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.4423 (pp) REVERT: M 44 ARG cc_start: 0.8214 (ttt180) cc_final: 0.7993 (tmt-80) REVERT: M 46 GLU cc_start: 0.8659 (tt0) cc_final: 0.8434 (pm20) REVERT: M 83 MET cc_start: 0.4105 (mmt) cc_final: 0.2161 (ptp) REVERT: M 118 VAL cc_start: 0.6736 (OUTLIER) cc_final: 0.5765 (m) outliers start: 76 outliers final: 43 residues processed: 239 average time/residue: 0.3720 time to fit residues: 146.5930 Evaluate side-chains 209 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 709 SER Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 99 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 335 optimal weight: 50.0000 chunk 83 optimal weight: 20.0000 chunk 146 optimal weight: 3.9990 chunk 336 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 HIS A 817 GLN B 159 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN ** H 5 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 = 0.3397 r_free = 0.3397 target = 0.047599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3017 r_free = 0.3017 target = 0.033535 restraints weight = 312163.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.034236 restraints weight = 181797.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.035057 restraints weight = 132790.093| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28774 Z= 0.155 Angle : 0.754 14.176 38982 Z= 0.378 Chirality : 0.046 0.328 4355 Planarity : 0.005 0.082 4945 Dihedral : 7.003 71.029 3873 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.21 % Favored : 89.45 % Rotamer: Outliers : 1.77 % Allowed : 18.58 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3545 helix: 0.46 (0.15), residues: 1226 sheet: -1.62 (0.21), residues: 563 loop : -2.39 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 796 HIS 0.006 0.001 HIS L 49 PHE 0.032 0.001 PHE L 62 TYR 0.019 0.002 TYR C 253 ARG 0.013 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 847) hydrogen bonds : angle 4.94244 ( 2424) SS BOND : bond 0.00429 ( 20) SS BOND : angle 1.99576 ( 40) covalent geometry : bond 0.00341 (28754) covalent geometry : angle 0.75174 (38942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 164 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8345 (p) REVERT: A 74 MET cc_start: 0.9471 (mtt) cc_final: 0.8986 (mmm) REVERT: A 125 MET cc_start: 0.7978 (ttt) cc_final: 0.7557 (ttt) REVERT: A 131 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7575 (tppt) REVERT: A 154 MET cc_start: 0.9268 (mtm) cc_final: 0.8693 (mtm) REVERT: A 230 MET cc_start: 0.9225 (mtm) cc_final: 0.8862 (mtt) REVERT: A 375 MET cc_start: 0.8745 (mmm) cc_final: 0.8021 (mmp) REVERT: A 583 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7227 (mt) REVERT: B 142 MET cc_start: 0.9117 (mtp) cc_final: 0.7604 (ptp) REVERT: B 537 MET cc_start: 0.8837 (tmm) cc_final: 0.8441 (tmm) REVERT: B 739 MET cc_start: 0.9297 (mmm) cc_final: 0.9000 (mmm) REVERT: B 797 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 74 MET cc_start: 0.9442 (mtt) cc_final: 0.8948 (mmm) REVERT: C 125 MET cc_start: 0.8112 (ttt) cc_final: 0.7752 (ttt) REVERT: C 154 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8474 (mtm) REVERT: C 230 MET cc_start: 0.9195 (mtp) cc_final: 0.8862 (ptp) REVERT: C 375 MET cc_start: 0.8776 (mmm) cc_final: 0.8024 (mmp) REVERT: C 583 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7203 (mt) REVERT: C 597 MET cc_start: 0.9631 (mmm) cc_final: 0.9385 (mtt) REVERT: C 727 MET cc_start: 0.8597 (mmm) cc_final: 0.8315 (mmp) REVERT: C 781 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9233 (mm) REVERT: D 54 HIS cc_start: 0.9105 (p-80) cc_final: 0.8867 (p-80) REVERT: D 142 MET cc_start: 0.9113 (mtp) cc_final: 0.7762 (ptp) REVERT: D 430 MET cc_start: 0.8493 (tmm) cc_final: 0.7487 (tmm) REVERT: D 537 MET cc_start: 0.8794 (tmm) cc_final: 0.8390 (tmm) REVERT: D 561 MET cc_start: 0.9272 (ptp) cc_final: 0.8796 (ptp) REVERT: H 109 PHE cc_start: 0.8643 (p90) cc_final: 0.8297 (p90) REVERT: M 20 LEU cc_start: 0.5766 (OUTLIER) cc_final: 0.4134 (pp) REVERT: M 46 GLU cc_start: 0.8529 (tt0) cc_final: 0.8307 (pm20) REVERT: M 83 MET cc_start: 0.3995 (mmt) cc_final: 0.2280 (ptp) REVERT: M 118 VAL cc_start: 0.6280 (OUTLIER) cc_final: 0.5477 (m) outliers start: 54 outliers final: 42 residues processed: 216 average time/residue: 0.4049 time to fit residues: 145.0524 Evaluate side-chains 211 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 3.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 183 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 246 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN B 159 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS C 817 GLN D 405 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN ** H 5 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 = 0.3416 r_free = 0.3416 target = 0.048141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.035907 restraints weight = 309744.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.035857 restraints weight = 181974.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.036302 restraints weight = 125329.533| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28774 Z= 0.129 Angle : 0.743 16.389 38982 Z= 0.371 Chirality : 0.045 0.251 4355 Planarity : 0.005 0.081 4945 Dihedral : 6.838 69.523 3873 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.01 % Favored : 89.56 % Rotamer: Outliers : 1.64 % Allowed : 18.97 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3545 helix: 0.57 (0.16), residues: 1226 sheet: -1.60 (0.22), residues: 555 loop : -2.32 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 610 HIS 0.006 0.001 HIS L 49 PHE 0.020 0.001 PHE L 97 TYR 0.019 0.001 TYR C 253 ARG 0.011 0.000 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.03323 ( 847) hydrogen bonds : angle 4.86565 ( 2424) SS BOND : bond 0.00373 ( 20) SS BOND : angle 1.86840 ( 40) covalent geometry : bond 0.00288 (28754) covalent geometry : angle 0.74068 (38942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7090 Ramachandran restraints generated. 3545 Oldfield, 0 Emsley, 3545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9471 (mtt) cc_final: 0.8984 (mmm) REVERT: A 125 MET cc_start: 0.7937 (ttt) cc_final: 0.7510 (ttt) REVERT: A 154 MET cc_start: 0.9323 (mtm) cc_final: 0.8723 (mtm) REVERT: A 230 MET cc_start: 0.9212 (mtm) cc_final: 0.8821 (mtt) REVERT: A 375 MET cc_start: 0.8710 (mmm) cc_final: 0.7994 (mmp) REVERT: A 583 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7230 (mt) REVERT: A 628 MET cc_start: 0.8582 (ppp) cc_final: 0.8352 (ppp) REVERT: B 142 MET cc_start: 0.8979 (mtp) cc_final: 0.7702 (ptp) REVERT: B 161 MET cc_start: 0.9010 (ppp) cc_final: 0.8323 (ppp) REVERT: B 486 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.8017 (p-80) REVERT: B 537 MET cc_start: 0.8840 (tmm) cc_final: 0.8434 (tmm) REVERT: B 739 MET cc_start: 0.9325 (mmm) cc_final: 0.9028 (mmm) REVERT: B 797 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8186 (mm) REVERT: C 74 MET cc_start: 0.9437 (mtt) cc_final: 0.8811 (mmm) REVERT: C 125 MET cc_start: 0.7978 (ttt) cc_final: 0.7589 (ttt) REVERT: C 154 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9137 (mtm) REVERT: C 375 MET cc_start: 0.8746 (mmm) cc_final: 0.7983 (mmp) REVERT: C 583 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7213 (mt) REVERT: C 597 MET cc_start: 0.9583 (mmm) cc_final: 0.9360 (mtt) REVERT: C 727 MET cc_start: 0.8578 (mmm) cc_final: 0.8292 (mmp) REVERT: D 142 MET cc_start: 0.8915 (mtp) cc_final: 0.7875 (ptm) REVERT: D 161 MET cc_start: 0.9028 (ppp) cc_final: 0.8385 (ppp) REVERT: D 430 MET cc_start: 0.8365 (tmm) cc_final: 0.7391 (tmm) REVERT: D 537 MET cc_start: 0.8853 (tmm) cc_final: 0.8446 (tmm) REVERT: D 561 MET cc_start: 0.9258 (ptp) cc_final: 0.8833 (ptp) REVERT: D 767 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6008 (mp-120) REVERT: L 92 ASP cc_start: 0.6434 (m-30) cc_final: 0.6174 (m-30) REVERT: M 20 LEU cc_start: 0.5662 (OUTLIER) cc_final: 0.3871 (pp) REVERT: M 46 GLU cc_start: 0.8524 (tt0) cc_final: 0.8304 (pm20) REVERT: M 83 MET cc_start: 0.3894 (mmt) cc_final: 0.2213 (ptp) REVERT: M 118 VAL cc_start: 0.6183 (OUTLIER) cc_final: 0.5411 (m) outliers start: 50 outliers final: 40 residues processed: 212 average time/residue: 0.3825 time to fit residues: 133.1105 Evaluate side-chains 205 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 797 LEU Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 808 VAL Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 118 VAL Chi-restraints excluded: chain N residue 50 TYR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 188 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 183 optimal weight: 0.9980 chunk 354 optimal weight: 50.0000 chunk 320 optimal weight: 40.0000 chunk 213 optimal weight: 8.9990 overall best weight: 5.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 GLN C 530 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 767 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 HIS ** L 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.046742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.034464 restraints weight = 315382.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.034350 restraints weight = 187505.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034837 restraints weight = 128878.058| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 28774 Z= 0.238 Angle : 0.813 14.676 38982 Z= 0.408 Chirality : 0.046 0.212 4355 Planarity : 0.005 0.082 4945 Dihedral : 7.031 71.534 3873 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.54 % Favored : 88.07 % Rotamer: Outliers : 1.73 % Allowed : 19.10 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.14), residues: 3545 helix: 0.48 (0.15), residues: 1228 sheet: -1.64 (0.21), residues: 587 loop : -2.44 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 796 HIS 0.006 0.001 HIS D 359 PHE 0.022 0.002 PHE B 529 TYR 0.027 0.002 TYR B 167 ARG 0.005 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 847) hydrogen bonds : angle 5.09837 ( 2424) SS BOND : bond 0.00468 ( 20) SS BOND : angle 1.86732 ( 40) covalent geometry : bond 0.00504 (28754) covalent geometry : angle 0.81116 (38942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12101.58 seconds wall clock time: 208 minutes 52.63 seconds (12532.63 seconds total)