Starting phenix.real_space_refine on Fri Mar 6 04:18:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7te9_25843/03_2026/7te9_25843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7te9_25843/03_2026/7te9_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_25843/03_2026/7te9_25843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7te9_25843/03_2026/7te9_25843.map" model { file = "/net/cci-nas-00/data/ceres_data/7te9_25843/03_2026/7te9_25843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7te9_25843/03_2026/7te9_25843.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.053 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 5, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'TYR: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: {'ASP:plan': 5, 'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'TYR: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: 6.19, per 1000 atoms: 0.22 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: 2.29 Conformation dependent library (CDL) restraints added in 1.3 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: 1.10 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: 5.47 Time building geometry restraints manager: 3.07 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.030 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (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 ARG 0.009 0.001 ARG B 375 TYR 0.034 0.003 TYR N 87 PHE 0.025 0.002 PHE D 529 TRP 0.027 0.003 TRP B 796 HIS 0.011 0.001 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00581 (28754) covalent geometry : angle 1.06137 (38942) SS BOND : bond 0.00730 ( 20) SS BOND : angle 1.99313 ( 40) hydrogen bonds : bond 0.19741 ( 847) hydrogen bonds : angle 8.08523 ( 2424) *********************** 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 : 1.168 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 230 MET cc_start: 0.9089 (mtm) cc_final: 0.8835 (mtt) REVERT: A 783 MET cc_start: 0.6818 (mtp) cc_final: 0.6521 (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: 0.6304 (mpp) REVERT: B 561 MET cc_start: 0.8882 (mmt) cc_final: 0.8638 (ttp) REVERT: B 824 MET cc_start: 0.7198 (mmt) cc_final: 0.6701 (mmm) REVERT: C 230 MET cc_start: 0.9122 (mtm) cc_final: 0.8916 (mtt) REVERT: C 347 MET cc_start: 0.9049 (ptp) cc_final: 0.8708 (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: 0.0440 (p) REVERT: H 110 ASP cc_start: 0.8926 (p0) cc_final: 0.8076 (t0) REVERT: L 61 ARG cc_start: 0.8104 (mtt90) cc_final: 0.7819 (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: 0.7399 (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: 0.1867 time to fit residues: 79.6759 Evaluate side-chains 188 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 177 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 425 HIS 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 697 ASN D 767 GLN H 5 GLN N 38 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.048202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.035885 restraints weight = 310684.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.035604 restraints weight = 181395.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.035986 restraints weight = 122941.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036159 restraints weight = 96416.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.036514 restraints weight = 85784.273| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 28774 Z= 0.275 Angle : 0.824 9.967 38982 Z= 0.434 Chirality : 0.046 0.240 4355 Planarity : 0.006 0.091 4945 Dihedral : 8.528 76.951 3883 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.93 % Favored : 89.65 % Rotamer: Outliers : 1.83 % Allowed : 11.61 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 9.86 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.13), residues: 3545 helix: -1.30 (0.14), residues: 1210 sheet: -1.84 (0.22), residues: 527 loop : -3.03 (0.12), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 431 TYR 0.025 0.002 TYR B 167 PHE 0.021 0.002 PHE B 563 TRP 0.029 0.002 TRP B 796 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00572 (28754) covalent geometry : angle 0.82275 (38942) SS BOND : bond 0.00491 ( 20) SS BOND : angle 1.64979 ( 40) hydrogen bonds : bond 0.04488 ( 847) hydrogen bonds : angle 5.83021 ( 2424) *********************** 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 : 1.141 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 125 MET cc_start: 0.8110 (ttt) cc_final: 0.7785 (ttt) REVERT: A 131 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7421 (tppt) REVERT: A 261 MET cc_start: 0.9244 (mmm) cc_final: 0.8932 (mmt) REVERT: A 533 MET cc_start: 0.8927 (mmm) cc_final: 0.8577 (tpt) REVERT: A 783 MET cc_start: 0.8072 (mtp) cc_final: 0.7767 (mtp) REVERT: B 73 MET cc_start: 0.8928 (tpp) cc_final: 0.8691 (mmm) REVERT: B 89 MET cc_start: 0.8474 (ptp) cc_final: 0.8175 (ppp) REVERT: B 157 MET cc_start: 0.9041 (mtt) cc_final: 0.8795 (mtp) REVERT: B 537 MET cc_start: 0.8930 (tmm) cc_final: 0.8641 (tmm) REVERT: B 565 MET cc_start: 0.8319 (mmm) cc_final: 0.8104 (mmm) REVERT: C 131 LYS cc_start: 0.8381 (mmtm) cc_final: 0.7773 (tppt) REVERT: C 230 MET cc_start: 0.9221 (mtm) cc_final: 0.8908 (mtt) REVERT: C 261 MET cc_start: 0.9111 (mmm) cc_final: 0.8563 (mmt) REVERT: C 423 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9052 (p) REVERT: C 533 MET cc_start: 0.8685 (mmm) cc_final: 0.8303 (mmm) REVERT: C 597 MET cc_start: 0.9618 (mmm) cc_final: 0.9259 (mtp) REVERT: C 839 MET cc_start: 0.8648 (ptm) cc_final: 0.8285 (ppp) REVERT: D 73 MET cc_start: 0.8998 (tpp) cc_final: 0.8648 (mmm) REVERT: D 157 MET cc_start: 0.9077 (mtt) cc_final: 0.8794 (mtp) REVERT: D 508 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8629 (mmm) REVERT: D 537 MET cc_start: 0.8951 (tmm) cc_final: 0.8658 (tmm) REVERT: D 739 MET cc_start: 0.9333 (mmm) cc_final: 0.9130 (mmm) REVERT: H 83 MET cc_start: 0.3791 (mmt) cc_final: 0.3478 (mmt) REVERT: H 110 ASP cc_start: 0.8866 (p0) cc_final: 0.8662 (t0) REVERT: L 82 ASP cc_start: 0.4767 (m-30) cc_final: 0.4504 (m-30) REVERT: M 83 MET cc_start: 0.3430 (mmt) cc_final: 0.2832 (mmt) REVERT: N 4 MET cc_start: 0.6326 (tmm) cc_final: 0.5625 (tmm) outliers start: 56 outliers final: 25 residues processed: 227 average time/residue: 0.1727 time to fit residues: 64.3754 Evaluate side-chains 199 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 647 SER Chi-restraints excluded: chain A residue 709 SER 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 508 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 150 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 647 SER 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 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 35 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 259 optimal weight: 0.0980 chunk 352 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 184 optimal weight: 0.0970 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 378 GLN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 334 ASN C 378 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 495 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.050058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.038099 restraints weight = 304133.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.038065 restraints weight = 176868.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.038590 restraints weight = 117736.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.038787 restraints weight = 90528.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.039146 restraints weight = 76343.514| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28774 Z= 0.118 Angle : 0.686 11.905 38982 Z= 0.360 Chirality : 0.045 0.186 4355 Planarity : 0.005 0.087 4945 Dihedral : 7.666 72.720 3877 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.66 % Favored : 90.86 % Rotamer: Outliers : 1.64 % Allowed : 13.15 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.13), residues: 3545 helix: -0.52 (0.15), residues: 1186 sheet: -1.71 (0.21), residues: 559 loop : -2.78 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 44 TYR 0.021 0.001 TYR H 95 PHE 0.017 0.001 PHE B 563 TRP 0.023 0.001 TRP B 796 HIS 0.005 0.001 HIS N 38 Details of bonding type rmsd covalent geometry : bond 0.00257 (28754) covalent geometry : angle 0.68452 (38942) SS BOND : bond 0.00245 ( 20) SS BOND : angle 1.73302 ( 40) hydrogen bonds : bond 0.03669 ( 847) hydrogen bonds : angle 5.16417 ( 2424) *********************** 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 231 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 0.764 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 125 MET cc_start: 0.8018 (ttt) cc_final: 0.7726 (ttt) REVERT: A 131 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7610 (tppt) REVERT: A 154 MET cc_start: 0.9195 (mtm) cc_final: 0.8900 (mtm) REVERT: A 230 MET cc_start: 0.9178 (mtm) cc_final: 0.8861 (mtt) REVERT: A 533 MET cc_start: 0.9089 (mmm) cc_final: 0.8663 (mmm) REVERT: A 781 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8862 (mt) REVERT: B 54 HIS cc_start: 0.9080 (p-80) cc_final: 0.8878 (p-80) REVERT: B 537 MET cc_start: 0.8824 (tmm) cc_final: 0.8345 (tmm) REVERT: B 565 MET cc_start: 0.8409 (mmm) cc_final: 0.8118 (mmm) REVERT: C 41 MET cc_start: 0.9033 (ptt) cc_final: 0.8752 (ppp) REVERT: C 230 MET cc_start: 0.9176 (mtm) cc_final: 0.8801 (mtt) REVERT: C 261 MET cc_start: 0.8966 (mmm) cc_final: 0.8518 (mmt) REVERT: C 597 MET cc_start: 0.9614 (mmm) cc_final: 0.9266 (mtm) REVERT: C 834 MET cc_start: 0.8121 (mpp) cc_final: 0.7775 (mpp) REVERT: C 839 MET cc_start: 0.8583 (ptm) cc_final: 0.8154 (ppp) REVERT: D 73 MET cc_start: 0.8968 (tpp) cc_final: 0.8722 (mmm) REVERT: D 537 MET cc_start: 0.8855 (tmm) cc_final: 0.8362 (tmm) REVERT: D 565 MET cc_start: 0.8421 (mmt) cc_final: 0.8205 (mmm) REVERT: D 739 MET cc_start: 0.9391 (mmm) cc_final: 0.9117 (mmm) REVERT: H 83 MET cc_start: 0.3891 (mmt) cc_final: 0.3669 (mmt) REVERT: H 110 ASP cc_start: 0.9276 (p0) cc_final: 0.9069 (t0) REVERT: M 83 MET cc_start: 0.3366 (mmt) cc_final: 0.2847 (mmt) outliers start: 50 outliers final: 20 residues processed: 219 average time/residue: 0.1708 time to fit residues: 60.7655 Evaluate side-chains 187 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 338 THR Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 61 HIS Chi-restraints excluded: chain B residue 486 HIS Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 579 PHE Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 486 HIS 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 H residue 4 LEU 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 121 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 125 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 156 optimal weight: 10.0000 chunk 259 optimal weight: 0.1980 overall best weight: 2.8388 ------------------------------------------------------------------------------- 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** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.048956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.036794 restraints weight = 306871.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.036703 restraints weight = 179127.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.037167 restraints weight = 120798.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.037299 restraints weight = 93562.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.037519 restraints weight = 83913.605| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28774 Z= 0.153 Angle : 0.695 13.088 38982 Z= 0.360 Chirality : 0.044 0.180 4355 Planarity : 0.005 0.085 4945 Dihedral : 7.361 72.375 3877 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.79 % Favored : 89.82 % Rotamer: Outliers : 1.83 % Allowed : 14.88 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.14), residues: 3545 helix: -0.07 (0.15), residues: 1200 sheet: -1.47 (0.22), residues: 531 loop : -2.67 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.019 0.001 TYR A 253 PHE 0.014 0.001 PHE D 563 TRP 0.027 0.001 TRP B 796 HIS 0.006 0.001 HIS N 38 Details of bonding type rmsd covalent geometry : bond 0.00330 (28754) covalent geometry : angle 0.69253 (38942) SS BOND : bond 0.00453 ( 20) SS BOND : angle 2.03455 ( 40) hydrogen bonds : bond 0.03398 ( 847) hydrogen bonds : angle 4.97844 ( 2424) *********************** 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 226 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 170 time to evaluate : 0.920 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: 0.9276 (mtt) cc_final: 0.8605 (mmm) REVERT: A 125 MET cc_start: 0.7958 (ttt) cc_final: 0.7605 (ttt) REVERT: A 131 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7627 (tppt) REVERT: A 230 MET cc_start: 0.9188 (mtm) cc_final: 0.8883 (mtt) REVERT: A 533 MET cc_start: 0.9199 (mmm) cc_final: 0.8887 (tpp) REVERT: B 54 HIS cc_start: 0.9107 (p-80) cc_final: 0.8878 (p-80) REVERT: B 89 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8466 (ppp) REVERT: B 307 MET cc_start: 0.8723 (tpt) cc_final: 0.8336 (tmm) REVERT: B 537 MET cc_start: 0.8821 (tmm) cc_final: 0.8413 (tmm) REVERT: B 561 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8558 (ttp) REVERT: B 565 MET cc_start: 0.8458 (mmm) cc_final: 0.8212 (mmm) REVERT: C 41 MET cc_start: 0.9102 (ptt) cc_final: 0.8766 (ppp) REVERT: C 74 MET cc_start: 0.9177 (mtt) cc_final: 0.8468 (mmm) REVERT: C 230 MET cc_start: 0.9185 (mtm) cc_final: 0.8898 (mtt) REVERT: C 261 MET cc_start: 0.9163 (mmm) cc_final: 0.8817 (mmt) REVERT: C 583 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7029 (mp) REVERT: C 597 MET cc_start: 0.9604 (mmm) cc_final: 0.9352 (mtm) REVERT: C 783 MET cc_start: 0.8396 (ttp) cc_final: 0.8164 (ttt) REVERT: C 839 MET cc_start: 0.8535 (ptm) cc_final: 0.8091 (ppp) REVERT: D 307 MET cc_start: 0.8741 (tpt) cc_final: 0.8284 (tmm) REVERT: D 537 MET cc_start: 0.8839 (tmm) cc_final: 0.8376 (tmm) REVERT: D 565 MET cc_start: 0.8658 (mmt) cc_final: 0.8448 (mmm) REVERT: D 739 MET cc_start: 0.9360 (mmm) cc_final: 0.9065 (mmm) REVERT: M 20 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.4147 (pp) REVERT: M 83 MET cc_start: 0.3423 (mmt) cc_final: 0.1260 (ptp) REVERT: M 118 VAL cc_start: 0.6948 (OUTLIER) cc_final: 0.5883 (m) REVERT: N 79 GLU cc_start: 0.5626 (OUTLIER) cc_final: 0.5272 (pm20) outliers start: 56 outliers final: 33 residues processed: 217 average time/residue: 0.1718 time to fit residues: 61.6547 Evaluate side-chains 202 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 338 THR 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 A residue 829 LEU 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 561 MET 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 583 LEU Chi-restraints excluded: chain C residue 647 SER 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 486 HIS Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS 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 H residue 37 VAL Chi-restraints excluded: chain H residue 44 ARG Chi-restraints excluded: chain M 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 79 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 218 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 326 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 188 optimal weight: 0.0040 overall best weight: 2.5798 ------------------------------------------------------------------------------- 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 703 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.048885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.037163 restraints weight = 308097.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.037147 restraints weight = 179166.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.037666 restraints weight = 119686.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.038089 restraints weight = 89075.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.038219 restraints weight = 74450.353| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28774 Z= 0.140 Angle : 0.676 14.045 38982 Z= 0.348 Chirality : 0.044 0.176 4355 Planarity : 0.005 0.083 4945 Dihedral : 7.125 71.318 3876 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.62 % Favored : 90.01 % Rotamer: Outliers : 2.13 % Allowed : 15.70 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.14), residues: 3545 helix: 0.16 (0.15), residues: 1222 sheet: -1.48 (0.21), residues: 555 loop : -2.60 (0.13), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 61 TYR 0.020 0.001 TYR C 253 PHE 0.013 0.001 PHE A 113 TRP 0.013 0.001 TRP D 796 HIS 0.008 0.001 HIS B 703 Details of bonding type rmsd covalent geometry : bond 0.00303 (28754) covalent geometry : angle 0.67435 (38942) SS BOND : bond 0.00367 ( 20) SS BOND : angle 1.76743 ( 40) hydrogen bonds : bond 0.03201 ( 847) hydrogen bonds : angle 4.80194 ( 2424) *********************** 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 231 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 166 time to evaluate : 1.180 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: 0.9332 (mtt) cc_final: 0.8667 (mmm) REVERT: A 125 MET cc_start: 0.7955 (ttt) cc_final: 0.7614 (ttt) REVERT: A 230 MET cc_start: 0.9188 (mtm) cc_final: 0.8876 (mtt) REVERT: B 54 HIS cc_start: 0.9127 (p-80) cc_final: 0.8855 (p-80) REVERT: B 89 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (ppp) REVERT: B 134 MET cc_start: 0.8151 (tmm) cc_final: 0.7938 (ppp) REVERT: B 474 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8325 (m-80) REVERT: B 537 MET cc_start: 0.8772 (tmm) cc_final: 0.8414 (tmm) REVERT: B 561 MET cc_start: 0.9366 (OUTLIER) cc_final: 0.8847 (ptm) REVERT: B 824 MET cc_start: 0.7191 (mmm) cc_final: 0.6953 (mmm) REVERT: C 41 MET cc_start: 0.9065 (ptt) cc_final: 0.8747 (ppp) REVERT: C 74 MET cc_start: 0.9283 (mtt) cc_final: 0.8629 (mmm) REVERT: C 230 MET cc_start: 0.9155 (mtm) cc_final: 0.8860 (mtt) REVERT: C 533 MET cc_start: 0.9205 (tpp) cc_final: 0.8973 (mmp) REVERT: C 597 MET cc_start: 0.9609 (mmm) cc_final: 0.9335 (mtp) REVERT: C 783 MET cc_start: 0.8241 (ttp) cc_final: 0.7899 (ttt) REVERT: C 834 MET cc_start: 0.8138 (mmm) cc_final: 0.7814 (mmm) REVERT: D 142 MET cc_start: 0.8971 (mtm) cc_final: 0.7985 (ptp) REVERT: D 537 MET cc_start: 0.8786 (tmm) cc_final: 0.8376 (tmm) REVERT: D 565 MET cc_start: 0.8744 (mmt) cc_final: 0.8498 (mmm) REVERT: D 739 MET cc_start: 0.9324 (mmm) cc_final: 0.9054 (mmm) REVERT: H 83 MET cc_start: 0.3803 (mmt) cc_final: 0.1890 (ptp) REVERT: M 20 LEU cc_start: 0.5829 (OUTLIER) cc_final: 0.3654 (pp) REVERT: M 83 MET cc_start: 0.3174 (mmt) cc_final: 0.1155 (ptp) REVERT: M 118 VAL cc_start: 0.6404 (OUTLIER) cc_final: 0.5407 (m) outliers start: 65 outliers final: 40 residues processed: 222 average time/residue: 0.1776 time to fit residues: 65.0989 Evaluate side-chains 208 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 539 THR Chi-restraints excluded: chain A residue 547 TYR 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 A residue 829 LEU 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 561 MET 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 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 647 SER Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 486 HIS 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 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 H residue 37 VAL Chi-restraints excluded: chain H residue 44 ARG 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 265 optimal weight: 30.0000 chunk 280 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 271 optimal weight: 0.7980 chunk 321 optimal weight: 6.9990 chunk 313 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 338 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN B 218 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 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 = 0.3388 r_free = 0.3388 target = 0.047222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.034023 restraints weight = 313315.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034206 restraints weight = 183256.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.034617 restraints weight = 128665.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.034741 restraints weight = 106034.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.034992 restraints weight = 95804.781| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 28774 Z= 0.229 Angle : 0.753 14.099 38982 Z= 0.387 Chirality : 0.044 0.200 4355 Planarity : 0.005 0.084 4945 Dihedral : 7.266 73.031 3876 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.63 % Favored : 89.03 % Rotamer: Outliers : 2.39 % Allowed : 16.42 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.14), residues: 3545 helix: 0.27 (0.15), residues: 1218 sheet: -1.53 (0.21), residues: 579 loop : -2.60 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.025 0.002 TYR B 167 PHE 0.015 0.002 PHE C 805 TRP 0.016 0.002 TRP A 519 HIS 0.006 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00480 (28754) covalent geometry : angle 0.75198 (38942) SS BOND : bond 0.00403 ( 20) SS BOND : angle 1.62659 ( 40) hydrogen bonds : bond 0.03586 ( 847) hydrogen bonds : angle 4.97562 ( 2424) *********************** 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 237 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 164 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9381 (mtt) cc_final: 0.8855 (mmm) REVERT: A 125 MET cc_start: 0.7995 (ttt) cc_final: 0.7569 (ttt) REVERT: A 131 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7549 (tppt) REVERT: A 154 MET cc_start: 0.9295 (mtm) cc_final: 0.8873 (mtm) REVERT: A 230 MET cc_start: 0.9184 (mtm) cc_final: 0.8902 (mtt) REVERT: A 375 MET cc_start: 0.8776 (mmm) cc_final: 0.8125 (mmp) REVERT: B 54 HIS cc_start: 0.9110 (p-80) cc_final: 0.8886 (p-80) REVERT: B 89 MET cc_start: 0.8962 (ptm) cc_final: 0.8564 (ppp) REVERT: B 142 MET cc_start: 0.8873 (mtm) cc_final: 0.7917 (ptm) REVERT: B 474 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.8051 (m-80) REVERT: B 537 MET cc_start: 0.8703 (tmm) cc_final: 0.8233 (tmm) REVERT: B 561 MET cc_start: 0.9237 (ttp) cc_final: 0.8986 (ptm) REVERT: B 739 MET cc_start: 0.9265 (mmm) cc_final: 0.9045 (mmm) REVERT: B 824 MET cc_start: 0.6960 (mmm) cc_final: 0.6695 (mmm) REVERT: C 74 MET cc_start: 0.9339 (mtt) cc_final: 0.8679 (mmm) REVERT: C 230 MET cc_start: 0.9162 (mtm) cc_final: 0.8896 (mtt) REVERT: C 375 MET cc_start: 0.8858 (mmm) cc_final: 0.8176 (mmp) REVERT: C 533 MET cc_start: 0.9068 (tpp) cc_final: 0.8729 (mmp) REVERT: C 597 MET cc_start: 0.9662 (mmm) cc_final: 0.9378 (mtp) REVERT: D 142 MET cc_start: 0.9068 (mtm) cc_final: 0.7931 (ptp) REVERT: D 474 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: D 537 MET cc_start: 0.8753 (tmm) cc_final: 0.8274 (tmm) REVERT: D 739 MET cc_start: 0.9243 (mmm) cc_final: 0.8978 (mmm) REVERT: H 83 MET cc_start: 0.4046 (mmt) cc_final: 0.3693 (mmt) REVERT: M 20 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.3534 (pp) REVERT: M 83 MET cc_start: 0.3485 (mmt) cc_final: 0.2064 (ptp) REVERT: M 118 VAL cc_start: 0.6222 (OUTLIER) cc_final: 0.5256 (m) outliers start: 73 outliers final: 52 residues processed: 229 average time/residue: 0.1751 time to fit residues: 66.7079 Evaluate side-chains 215 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 539 THR Chi-restraints excluded: chain A residue 547 TYR 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 702 TYR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 829 LEU 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 767 GLN 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 647 SER 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 829 LEU 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 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 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 H residue 37 VAL Chi-restraints excluded: chain H residue 44 ARG 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 79 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 349 optimal weight: 5.9990 chunk 278 optimal weight: 3.9990 chunk 328 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 315 optimal weight: 50.0000 chunk 184 optimal weight: 7.9990 chunk 158 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN M 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.047135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.034813 restraints weight = 312086.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.034725 restraints weight = 184792.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035180 restraints weight = 126710.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.035345 restraints weight = 100187.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.035754 restraints weight = 88249.677| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3547 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= 0.213 Angle : 0.753 11.400 38982 Z= 0.386 Chirality : 0.045 0.190 4355 Planarity : 0.005 0.084 4945 Dihedral : 7.245 72.793 3876 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.41 % Favored : 89.25 % Rotamer: Outliers : 2.22 % Allowed : 17.34 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 8.45 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.14), residues: 3545 helix: 0.32 (0.15), residues: 1226 sheet: -1.50 (0.21), residues: 573 loop : -2.64 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 61 TYR 0.021 0.002 TYR B 167 PHE 0.013 0.001 PHE C 838 TRP 0.016 0.001 TRP D 796 HIS 0.006 0.001 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00452 (28754) covalent geometry : angle 0.75026 (38942) SS BOND : bond 0.00516 ( 20) SS BOND : angle 2.08299 ( 40) hydrogen bonds : bond 0.03615 ( 847) hydrogen bonds : angle 4.99724 ( 2424) *********************** 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: 68 poor density : 162 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9409 (mtt) cc_final: 0.8893 (mmm) REVERT: A 125 MET cc_start: 0.8006 (ttt) cc_final: 0.7600 (ttt) REVERT: A 131 LYS cc_start: 0.7814 (mmtm) cc_final: 0.7555 (tppt) REVERT: A 230 MET cc_start: 0.9185 (mtm) cc_final: 0.8924 (mtt) REVERT: A 662 MET cc_start: 0.9433 (tmm) cc_final: 0.9142 (ppp) REVERT: B 54 HIS cc_start: 0.9190 (p-80) cc_final: 0.8948 (p-80) REVERT: B 89 MET cc_start: 0.9136 (ptm) cc_final: 0.8712 (ppp) REVERT: B 142 MET cc_start: 0.8859 (mtm) cc_final: 0.7932 (ptm) REVERT: B 474 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: B 537 MET cc_start: 0.8725 (tmm) cc_final: 0.8416 (tmm) REVERT: B 797 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7927 (mm) REVERT: B 824 MET cc_start: 0.6838 (mmm) cc_final: 0.6569 (mmm) REVERT: C 74 MET cc_start: 0.9419 (mtt) cc_final: 0.8943 (mmm) REVERT: C 154 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8570 (mtm) REVERT: C 230 MET cc_start: 0.9171 (mtm) cc_final: 0.8908 (mtt) REVERT: C 375 MET cc_start: 0.8861 (mmm) cc_final: 0.8238 (mmp) REVERT: C 597 MET cc_start: 0.9635 (mmm) cc_final: 0.9377 (mtp) REVERT: D 142 MET cc_start: 0.9048 (mtm) cc_final: 0.7812 (ptp) REVERT: D 474 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: D 537 MET cc_start: 0.8768 (tmm) cc_final: 0.8439 (tmm) REVERT: D 561 MET cc_start: 0.9246 (ptp) cc_final: 0.8927 (ptp) REVERT: D 739 MET cc_start: 0.9246 (mmm) cc_final: 0.8926 (mmm) REVERT: H 83 MET cc_start: 0.4275 (mmt) cc_final: 0.3818 (mmt) REVERT: M 20 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.4264 (pp) REVERT: M 83 MET cc_start: 0.3699 (mmt) cc_final: 0.1710 (ptp) REVERT: M 118 VAL cc_start: 0.6724 (OUTLIER) cc_final: 0.5818 (m) outliers start: 68 outliers final: 52 residues processed: 222 average time/residue: 0.1760 time to fit residues: 64.5827 Evaluate side-chains 216 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 158 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 539 THR Chi-restraints excluded: chain A residue 547 TYR 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 702 TYR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 MET Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 829 LEU 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 767 GLN 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 647 SER Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 781 ILE Chi-restraints excluded: chain C residue 829 LEU 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 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 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 H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 111 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 79 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 192 optimal weight: 0.3980 chunk 172 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 326 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3420 r_free = 0.3420 target = 0.048243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.036973 restraints weight = 310110.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.036875 restraints weight = 187200.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.037360 restraints weight = 121115.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.037825 restraints weight = 88941.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.037914 restraints weight = 73624.819| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28774 Z= 0.125 Angle : 0.716 13.519 38982 Z= 0.362 Chirality : 0.045 0.275 4355 Planarity : 0.005 0.082 4945 Dihedral : 6.971 70.363 3876 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.90 % Favored : 89.73 % Rotamer: Outliers : 2.00 % Allowed : 17.86 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 6.34 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.14), residues: 3545 helix: 0.56 (0.16), residues: 1220 sheet: -1.56 (0.21), residues: 555 loop : -2.46 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 61 TYR 0.019 0.001 TYR C 253 PHE 0.021 0.001 PHE L 62 TRP 0.021 0.001 TRP L 35 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00280 (28754) covalent geometry : angle 0.71361 (38942) SS BOND : bond 0.00355 ( 20) SS BOND : angle 1.90351 ( 40) hydrogen bonds : bond 0.03397 ( 847) hydrogen bonds : angle 4.78727 ( 2424) *********************** 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 225 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 164 time to evaluate : 1.202 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: 0.9407 (mtt) cc_final: 0.8922 (mmm) REVERT: A 125 MET cc_start: 0.8000 (ttt) cc_final: 0.7558 (ttt) REVERT: A 154 MET cc_start: 0.9315 (mtm) cc_final: 0.8781 (mtm) REVERT: A 230 MET cc_start: 0.9223 (mtm) cc_final: 0.8876 (mtt) REVERT: A 375 MET cc_start: 0.8683 (mmm) cc_final: 0.7876 (mmp) REVERT: B 54 HIS cc_start: 0.9060 (p-80) cc_final: 0.8733 (p-80) REVERT: B 89 MET cc_start: 0.9085 (ptm) cc_final: 0.8591 (ppp) REVERT: B 142 MET cc_start: 0.8793 (mtm) cc_final: 0.7930 (ptm) REVERT: B 307 MET cc_start: 0.8583 (tpt) cc_final: 0.8361 (tmm) REVERT: B 508 MET cc_start: 0.8783 (mmm) cc_final: 0.8408 (mmp) REVERT: B 537 MET cc_start: 0.8798 (tmm) cc_final: 0.8425 (tmm) REVERT: B 797 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7890 (mm) REVERT: B 824 MET cc_start: 0.6474 (mmm) cc_final: 0.6260 (mmm) REVERT: C 74 MET cc_start: 0.9415 (mtt) cc_final: 0.8924 (mmm) REVERT: C 154 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9125 (mtm) REVERT: C 230 MET cc_start: 0.9214 (mtm) cc_final: 0.8884 (mtt) REVERT: C 597 MET cc_start: 0.9602 (mmm) cc_final: 0.9346 (mtp) REVERT: D 142 MET cc_start: 0.8960 (mtm) cc_final: 0.7773 (ptp) REVERT: D 486 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7854 (p-80) REVERT: D 537 MET cc_start: 0.8770 (tmm) cc_final: 0.8392 (tmm) REVERT: D 561 MET cc_start: 0.9230 (ptp) cc_final: 0.8964 (ptp) REVERT: D 565 MET cc_start: 0.8746 (mmt) cc_final: 0.8512 (mpp) REVERT: D 739 MET cc_start: 0.9271 (mmm) cc_final: 0.8953 (mmm) REVERT: H 51 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6306 (tt) REVERT: H 83 MET cc_start: 0.3384 (mmt) cc_final: 0.2742 (mmt) REVERT: M 20 LEU cc_start: 0.5136 (OUTLIER) cc_final: 0.2766 (pp) REVERT: M 83 MET cc_start: 0.2640 (mmt) cc_final: 0.1050 (ptp) REVERT: M 118 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.5982 (m) outliers start: 61 outliers final: 42 residues processed: 219 average time/residue: 0.1824 time to fit residues: 65.6321 Evaluate side-chains 209 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 829 LEU 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 767 GLN 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 656 VAL Chi-restraints excluded: chain C residue 675 PHE Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 345 GLU Chi-restraints excluded: chain D residue 486 HIS 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 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 H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 111 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 311 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 319 optimal weight: 50.0000 chunk 213 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 243 optimal weight: 0.4980 chunk 202 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 343 optimal weight: 40.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 376 ASN B 405 HIS ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** 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 = 0.3438 r_free = 0.3438 target = 0.048756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.035875 restraints weight = 309201.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.036055 restraints weight = 179735.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.036471 restraints weight = 126676.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.036984 restraints weight = 100411.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.037143 restraints weight = 89035.773| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28774 Z= 0.115 Angle : 0.724 14.115 38982 Z= 0.361 Chirality : 0.045 0.328 4355 Planarity : 0.004 0.079 4945 Dihedral : 6.730 68.489 3875 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 9.28 % Favored : 90.27 % Rotamer: Outliers : 1.73 % Allowed : 18.19 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3545 helix: 0.59 (0.16), residues: 1222 sheet: -1.42 (0.22), residues: 531 loop : -2.38 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 784 TYR 0.019 0.001 TYR A 253 PHE 0.014 0.001 PHE A 113 TRP 0.017 0.001 TRP L 35 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00256 (28754) covalent geometry : angle 0.72220 (38942) SS BOND : bond 0.00348 ( 20) SS BOND : angle 1.75882 ( 40) hydrogen bonds : bond 0.03354 ( 847) hydrogen bonds : angle 4.75140 ( 2424) *********************** 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 223 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 1.143 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: 0.9432 (mtt) cc_final: 0.8925 (mmm) REVERT: A 125 MET cc_start: 0.7948 (ttt) cc_final: 0.7481 (ttt) REVERT: A 154 MET cc_start: 0.9283 (mtm) cc_final: 0.8507 (mtm) REVERT: A 230 MET cc_start: 0.9207 (mtm) cc_final: 0.8820 (mtt) REVERT: A 375 MET cc_start: 0.8716 (mmm) cc_final: 0.7929 (mmp) REVERT: B 54 HIS cc_start: 0.9141 (p-80) cc_final: 0.8889 (p-80) REVERT: B 89 MET cc_start: 0.9146 (ptm) cc_final: 0.8677 (ppp) REVERT: B 142 MET cc_start: 0.8863 (mtm) cc_final: 0.7826 (ptm) REVERT: B 486 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7948 (p-80) REVERT: B 537 MET cc_start: 0.8776 (tmm) cc_final: 0.8357 (tmm) REVERT: B 797 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7963 (mm) REVERT: B 824 MET cc_start: 0.6356 (mmm) cc_final: 0.6111 (mmm) REVERT: C 74 MET cc_start: 0.9435 (mtt) cc_final: 0.8812 (mmm) REVERT: C 154 MET cc_start: 0.9349 (OUTLIER) cc_final: 0.9127 (mtm) REVERT: C 230 MET cc_start: 0.9190 (mtm) cc_final: 0.8838 (mtt) REVERT: C 375 MET cc_start: 0.8781 (mmm) cc_final: 0.7804 (mmp) REVERT: C 597 MET cc_start: 0.9598 (mmm) cc_final: 0.9366 (mtp) REVERT: C 781 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8808 (mm) REVERT: C 834 MET cc_start: 0.8377 (mmp) cc_final: 0.7733 (mmp) REVERT: D 142 MET cc_start: 0.8961 (mtm) cc_final: 0.7739 (ptp) REVERT: D 537 MET cc_start: 0.8810 (tmm) cc_final: 0.8355 (tmm) REVERT: D 565 MET cc_start: 0.8754 (mmt) cc_final: 0.8484 (mpp) REVERT: D 739 MET cc_start: 0.9284 (mmm) cc_final: 0.9004 (mmm) REVERT: D 829 MET cc_start: 0.9444 (ptp) cc_final: 0.8996 (ppp) REVERT: H 83 MET cc_start: 0.4555 (mmt) cc_final: 0.4162 (mmt) REVERT: L 47 LEU cc_start: 0.0771 (OUTLIER) cc_final: -0.0279 (mm) REVERT: L 92 ASP cc_start: 0.6379 (m-30) cc_final: 0.6159 (m-30) REVERT: M 20 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.4175 (pp) REVERT: M 83 MET cc_start: 0.3734 (mmt) cc_final: 0.1820 (ptp) REVERT: M 118 VAL cc_start: 0.6181 (OUTLIER) cc_final: 0.5384 (m) REVERT: N 92 ASP cc_start: 0.7263 (m-30) cc_final: 0.7048 (m-30) outliers start: 53 outliers final: 39 residues processed: 220 average time/residue: 0.1789 time to fit residues: 64.6971 Evaluate side-chains 210 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 829 LEU 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 767 GLN 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 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 656 VAL Chi-restraints excluded: chain C residue 675 PHE 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 560 VAL Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 746 CYS 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 H residue 111 VAL Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 101 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 6 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 296 optimal weight: 0.7980 chunk 300 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 324 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 376 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3433 r_free = 0.3433 target = 0.048496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.034668 restraints weight = 309400.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.035375 restraints weight = 182733.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.035808 restraints weight = 131060.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.036448 restraints weight = 107993.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.036533 restraints weight = 96142.842| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28774 Z= 0.125 Angle : 0.730 14.714 38982 Z= 0.362 Chirality : 0.045 0.268 4355 Planarity : 0.004 0.079 4945 Dihedral : 6.580 68.294 3873 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.45 % Favored : 90.18 % Rotamer: Outliers : 1.44 % Allowed : 18.25 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.14), residues: 3545 helix: 0.62 (0.16), residues: 1230 sheet: -1.47 (0.22), residues: 521 loop : -2.32 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 61 TYR 0.021 0.001 TYR H 95 PHE 0.016 0.001 PHE L 62 TRP 0.016 0.001 TRP L 35 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00279 (28754) covalent geometry : angle 0.72822 (38942) SS BOND : bond 0.00364 ( 20) SS BOND : angle 1.65497 ( 40) hydrogen bonds : bond 0.03253 ( 847) hydrogen bonds : angle 4.75207 ( 2424) ********************** 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 206 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 1.045 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: 0.9456 (mtp) cc_final: 0.8956 (mmm) REVERT: A 125 MET cc_start: 0.7923 (ttt) cc_final: 0.7443 (ttt) REVERT: A 154 MET cc_start: 0.9271 (mtm) cc_final: 0.8511 (mtm) REVERT: A 230 MET cc_start: 0.9143 (mtm) cc_final: 0.8881 (mtt) REVERT: A 375 MET cc_start: 0.8703 (mmm) cc_final: 0.7926 (mmp) REVERT: B 89 MET cc_start: 0.9188 (ptm) cc_final: 0.8715 (ppp) REVERT: B 142 MET cc_start: 0.8939 (mtm) cc_final: 0.7858 (ptm) REVERT: B 486 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7921 (p-80) REVERT: B 537 MET cc_start: 0.8762 (tmm) cc_final: 0.8386 (tmm) REVERT: B 797 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 824 MET cc_start: 0.6250 (mmm) cc_final: 0.6032 (mmm) REVERT: C 74 MET cc_start: 0.9439 (mtt) cc_final: 0.8931 (mmm) REVERT: C 154 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9050 (mtm) REVERT: C 230 MET cc_start: 0.9163 (mtm) cc_final: 0.8834 (mtt) REVERT: C 375 MET cc_start: 0.8767 (mmm) cc_final: 0.7822 (mmp) REVERT: C 597 MET cc_start: 0.9621 (mmm) cc_final: 0.9387 (mtp) REVERT: C 834 MET cc_start: 0.8484 (mmp) cc_final: 0.7848 (mmm) REVERT: D 142 MET cc_start: 0.9020 (mtm) cc_final: 0.7699 (ptp) REVERT: D 537 MET cc_start: 0.8761 (tmm) cc_final: 0.8353 (tmm) REVERT: D 565 MET cc_start: 0.8732 (mmt) cc_final: 0.8474 (mpp) REVERT: D 739 MET cc_start: 0.9211 (mmm) cc_final: 0.8938 (mmm) REVERT: D 829 MET cc_start: 0.9418 (ptp) cc_final: 0.8913 (ppp) REVERT: H 83 MET cc_start: 0.4476 (mmt) cc_final: 0.4141 (mmt) REVERT: H 109 PHE cc_start: 0.8658 (p90) cc_final: 0.8368 (p90) REVERT: M 20 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.4203 (pp) REVERT: M 83 MET cc_start: 0.3803 (mmt) cc_final: 0.1951 (ptp) REVERT: M 118 VAL cc_start: 0.6208 (OUTLIER) cc_final: 0.5414 (m) outliers start: 44 outliers final: 36 residues processed: 204 average time/residue: 0.1793 time to fit residues: 60.0030 Evaluate side-chains 202 residues out of total 3111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 547 TYR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 675 PHE Chi-restraints excluded: chain A residue 702 TYR Chi-restraints excluded: chain A residue 765 CYS Chi-restraints excluded: chain A residue 829 LEU 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 39 GLU Chi-restraints excluded: chain C residue 65 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 675 PHE Chi-restraints excluded: chain C residue 702 TYR Chi-restraints excluded: chain C residue 765 CYS Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 345 GLU 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 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 H residue 79 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 207 optimal weight: 4.9990 chunk 304 optimal weight: 0.0670 chunk 213 optimal weight: 8.9990 chunk 256 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 345 optimal weight: 20.0000 chunk 93 optimal weight: 0.2980 chunk 280 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 overall best weight: 1.3920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 376 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN B 767 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 ASN ** 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 697 ASN ** 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 = 0.3447 r_free = 0.3447 target = 0.048871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.036151 restraints weight = 309767.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.036300 restraints weight = 178913.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.036752 restraints weight = 125369.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.036941 restraints weight = 101358.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037298 restraints weight = 87700.117| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4132 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 : 0.729 14.591 38982 Z= 0.358 Chirality : 0.045 0.265 4355 Planarity : 0.004 0.078 4945 Dihedral : 6.419 66.830 3872 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.83 % Favored : 90.80 % Rotamer: Outliers : 1.37 % Allowed : 18.65 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.06 % Twisted Proline : 5.63 % Twisted General : 0.47 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3545 helix: 0.79 (0.16), residues: 1210 sheet: -1.47 (0.22), residues: 551 loop : -2.26 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 44 TYR 0.019 0.001 TYR H 95 PHE 0.024 0.001 PHE L 97 TRP 0.015 0.001 TRP L 35 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00254 (28754) covalent geometry : angle 0.72750 (38942) SS BOND : bond 0.00341 ( 20) SS BOND : angle 1.60835 ( 40) hydrogen bonds : bond 0.03177 ( 847) hydrogen bonds : angle 4.65796 ( 2424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6048.24 seconds wall clock time: 104 minutes 51.37 seconds (6291.37 seconds total)