Starting phenix.real_space_refine on Thu Mar 5 16:57:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ira_9714/03_2026/6ira_9714_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ira_9714/03_2026/6ira_9714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ira_9714/03_2026/6ira_9714_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ira_9714/03_2026/6ira_9714_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ira_9714/03_2026/6ira_9714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ira_9714/03_2026/6ira_9714.map" } resolution = 4.5 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= 0.018 sd= 1.311 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 142 5.16 5 C 15358 2.51 5 N 4040 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 23932 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'TRP:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'TRP:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 5907 Chain: "A" Number of atoms: 6175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 6290 Chain: "B" Number of atoms: 5791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'TRP:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'TRP:plan': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 5907 Chain: "C" Number of atoms: 6175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 6290 Time building chain proxies: 9.31, per 1000 atoms: 0.39 Number of scatterers: 23932 At special positions: 0 Unit cell: (111.1, 146.45, 187.86, 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 142 16.00 O 4392 8.00 N 4040 7.00 C 15358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " 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: 1.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 36 sheets defined 43.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'D' and resid 45 through 60 Proline residue: D 57 - end of helix removed outlier: 4.296A pdb=" N ALA D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.513A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 116 " --> pdb=" O MET D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.597A pdb=" N TYR D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.877A pdb=" N SER D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.765A pdb=" N SER D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.812A pdb=" N ARG D 291 " --> pdb=" O SER D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 515 through 522 removed outlier: 3.840A pdb=" N VAL D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 581 Processing helix chain 'D' and resid 602 through 613 removed outlier: 3.811A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 611 " --> pdb=" O LEU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 653 removed outlier: 3.693A pdb=" N VAL D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TRP D 634 " --> pdb=" O MET D 630 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR D 645 " --> pdb=" O PHE D 641 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 649 " --> pdb=" O TYR D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 673 through 676 Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 698 through 706 Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.722A pdb=" N ALA D 716 " --> pdb=" O GLY D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.654A pdb=" N GLY D 740 " --> pdb=" O ASN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 785 removed outlier: 3.512A pdb=" N ILE D 775 " --> pdb=" O TRP D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 799 through 803 Processing helix chain 'D' and resid 819 through 836 removed outlier: 3.556A pdb=" N ILE D 836 " --> pdb=" O LEU D 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.772A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.466A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.927A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.608A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.612A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.693A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.536A pdb=" N ALA A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.552A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.801A pdb=" N ALA A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 4.344A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 580 Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.558A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 657 removed outlier: 3.850A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.717A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.906A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.683A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.558A pdb=" N LYS A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.772A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 60 Proline residue: B 57 - end of helix removed outlier: 4.411A pdb=" N ALA B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.539A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.613A pdb=" N TYR B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.872A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.800A pdb=" N SER B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.770A pdb=" N ARG B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.501A pdb=" N ASP B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.618A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 579 Processing helix chain 'B' and resid 602 through 613 removed outlier: 3.916A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 653 removed outlier: 3.612A pdb=" N MET B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 645 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 649 " --> pdb=" O TYR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.751A pdb=" N ALA B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.613A pdb=" N GLY B 740 " --> pdb=" O ASN B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 785 removed outlier: 3.510A pdb=" N ILE B 775 " --> pdb=" O TRP B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 799 through 803 Processing helix chain 'B' and resid 819 through 837 removed outlier: 3.632A pdb=" N ILE B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP B 837 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.772A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 104 through 113 removed outlier: 4.466A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.928A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.609A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.613A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.693A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.545A pdb=" N ALA C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.552A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.801A pdb=" N ALA C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 4.344A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 580 Processing helix chain 'C' and resid 604 through 615 removed outlier: 3.555A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 657 removed outlier: 3.850A pdb=" N LEU C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.716A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.906A pdb=" N TYR C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.683A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.558A pdb=" N LYS C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 810 through 844 removed outlier: 3.773A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 68 through 73 removed outlier: 3.973A pdb=" N GLY D 101 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU D 98 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE D 127 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N PHE D 100 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 199 through 205 removed outlier: 8.542A pdb=" N PHE D 170 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL D 226 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 230 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 229 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 277 through 280 removed outlier: 6.202A pdb=" N VAL D 365 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS D 374 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'D' and resid 405 through 410 Processing sheet with id=AA6, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'D' and resid 523 through 524 Processing sheet with id=AA8, first strand: chain 'D' and resid 682 through 683 removed outlier: 4.298A pdb=" N GLY D 683 " --> pdb=" O ALA D 727 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 729 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 534 " --> pdb=" O TYR D 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 60 through 62 removed outlier: 5.995A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 120 removed outlier: 6.406A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.610A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.241A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.674A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.680A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.680A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AB8, first strand: chain 'A' and resid 487 through 490 removed outlier: 4.560A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.742A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 3.902A pdb=" N GLY B 97 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 37 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 101 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 127 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE B 100 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 199 through 205 removed outlier: 8.652A pdb=" N PHE B 170 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 230 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 277 through 280 removed outlier: 6.116A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AC5, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.508A pdb=" N ASP B 476 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AC7, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AC8, first strand: chain 'B' and resid 728 through 731 Processing sheet with id=AC9, first strand: chain 'C' and resid 60 through 62 removed outlier: 5.996A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.406A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.610A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.242A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.674A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 478 removed outlier: 5.681A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 473 through 478 removed outlier: 5.681A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AD8, first strand: chain 'C' and resid 487 through 490 removed outlier: 4.560A pdb=" N LYS C 495 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 728 through 732 removed outlier: 3.742A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 2.44 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: 4757 1.33 - 1.45: 6454 1.45 - 1.58: 12983 1.58 - 1.70: 0 1.70 - 1.83: 248 Bond restraints: 24442 Sorted by residual: bond pdb=" C LYS B 628 " pdb=" N ILE B 629 " ideal model delta sigma weight residual 1.333 1.445 -0.112 1.31e-02 5.83e+03 7.28e+01 bond pdb=" C GLY B 753 " pdb=" N TYR B 754 " ideal model delta sigma weight residual 1.331 1.444 -0.114 1.45e-02 4.76e+03 6.16e+01 bond pdb=" C GLY D 753 " pdb=" N TYR D 754 " ideal model delta sigma weight residual 1.331 1.444 -0.114 1.45e-02 4.76e+03 6.15e+01 bond pdb=" C SER D 519 " pdb=" N GLU D 520 " ideal model delta sigma weight residual 1.335 1.233 0.102 1.31e-02 5.83e+03 6.02e+01 bond pdb=" N THR A 230 " pdb=" CA THR A 230 " ideal model delta sigma weight residual 1.459 1.375 0.084 1.20e-02 6.94e+03 4.96e+01 ... (remaining 24437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 32737 5.00 - 9.99: 362 9.99 - 14.99: 25 14.99 - 19.98: 4 19.98 - 24.98: 4 Bond angle restraints: 33132 Sorted by residual: angle pdb=" CA VAL C 246 " pdb=" C VAL C 246 " pdb=" N TRP C 247 " ideal model delta sigma weight residual 116.16 140.99 -24.83 9.60e-01 1.09e+00 6.69e+02 angle pdb=" CA VAL A 246 " pdb=" C VAL A 246 " pdb=" N TRP A 247 " ideal model delta sigma weight residual 116.16 140.97 -24.81 9.60e-01 1.09e+00 6.68e+02 angle pdb=" O VAL C 246 " pdb=" C VAL C 246 " pdb=" N TRP C 247 " ideal model delta sigma weight residual 122.67 97.69 24.98 1.04e+00 9.25e-01 5.77e+02 angle pdb=" O VAL A 246 " pdb=" C VAL A 246 " pdb=" N TRP A 247 " ideal model delta sigma weight residual 122.67 97.70 24.97 1.04e+00 9.25e-01 5.76e+02 angle pdb=" N PRO B 64 " pdb=" CA PRO B 64 " pdb=" C PRO B 64 " ideal model delta sigma weight residual 113.53 94.97 18.56 1.39e+00 5.18e-01 1.78e+02 ... (remaining 33127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 14030 16.27 - 32.53: 465 32.53 - 48.80: 11 48.80 - 65.06: 4 65.06 - 81.33: 4 Dihedral angle restraints: 14514 sinusoidal: 5578 harmonic: 8936 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual -86.00 -167.33 81.33 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -166.79 80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual -86.00 -164.15 78.15 1 1.00e+01 1.00e-02 7.63e+01 ... (remaining 14511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3321 0.105 - 0.209: 400 0.209 - 0.314: 49 0.314 - 0.418: 18 0.418 - 0.523: 2 Chirality restraints: 3790 Sorted by residual: chirality pdb=" CA PHE B 636 " pdb=" N PHE B 636 " pdb=" C PHE B 636 " pdb=" CB PHE B 636 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" CA PHE D 636 " pdb=" N PHE D 636 " pdb=" C PHE D 636 " pdb=" CB PHE D 636 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA GLU C 210 " pdb=" N GLU C 210 " pdb=" C GLU C 210 " pdb=" CB GLU C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 3787 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 628 " 0.043 2.00e-02 2.50e+03 9.47e-02 8.96e+01 pdb=" C LYS B 628 " -0.163 2.00e-02 2.50e+03 pdb=" O LYS B 628 " 0.069 2.00e-02 2.50e+03 pdb=" N ILE B 629 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 247 " -0.038 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C TRP C 247 " 0.121 2.00e-02 2.50e+03 pdb=" O TRP C 247 " -0.043 2.00e-02 2.50e+03 pdb=" N LEU C 248 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 247 " 0.038 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C TRP A 247 " -0.121 2.00e-02 2.50e+03 pdb=" O TRP A 247 " 0.043 2.00e-02 2.50e+03 pdb=" N LEU A 248 " 0.040 2.00e-02 2.50e+03 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 20 2.11 - 2.81: 6704 2.81 - 3.51: 32266 3.51 - 4.20: 54312 4.20 - 4.90: 87899 Nonbonded interactions: 181201 Sorted by model distance: nonbonded pdb=" O VAL D 535 " pdb=" N ILE D 750 " model vdw 1.413 3.120 nonbonded pdb=" O VAL B 535 " pdb=" N ILE B 750 " model vdw 1.423 3.120 nonbonded pdb=" OH TYR C 232 " pdb=" CB ALA C 262 " model vdw 1.439 3.460 nonbonded pdb=" O ALA C 228 " pdb=" CB TYR C 232 " model vdw 1.448 2.752 nonbonded pdb=" CG1 VAL B 522 " pdb=" O LEU B 765 " model vdw 1.621 3.460 ... (remaining 181196 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 775 or resid 777 through 844)) selection = (chain 'C' and (resid 25 through 775 or resid 777 through 844)) } ncs_group { reference = (chain 'B' and (resid 34 through 700 or resid 702 through 841)) selection = (chain 'D' and (resid 34 through 700 or resid 702 through 841)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 26.570 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.070 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 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 : 0.009 0.114 24452 Z= 0.470 Angle : 1.419 24.980 33152 Z= 0.909 Chirality : 0.075 0.523 3790 Planarity : 0.008 0.115 4182 Dihedral : 8.452 53.892 8704 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.02 % Favored : 89.12 % Rotamer: Outliers : 0.12 % Allowed : 0.16 % Favored : 99.72 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.53 (0.13), residues: 3028 helix: -2.37 (0.11), residues: 1212 sheet: -0.84 (0.29), residues: 300 loop : -2.64 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 839 TYR 0.052 0.005 TYR D 180 PHE 0.082 0.005 PHE B 580 TRP 0.050 0.006 TRP C 151 HIS 0.015 0.004 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00870 (24442) covalent geometry : angle 1.41886 (33132) SS BOND : bond 0.00443 ( 10) SS BOND : angle 1.85432 ( 20) hydrogen bonds : bond 0.18575 ( 1019) hydrogen bonds : angle 8.85669 ( 2959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1033 time to evaluate : 0.906 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 104 THR cc_start: 0.7161 (p) cc_final: 0.6777 (p) REVERT: D 133 MET cc_start: 0.8117 (mmm) cc_final: 0.7830 (mmm) REVERT: D 150 SER cc_start: 0.8393 (p) cc_final: 0.7162 (t) REVERT: D 199 ASP cc_start: 0.8264 (m-30) cc_final: 0.7904 (p0) REVERT: D 212 ASP cc_start: 0.7877 (m-30) cc_final: 0.7497 (m-30) REVERT: D 248 LEU cc_start: 0.8011 (mt) cc_final: 0.7570 (mt) REVERT: D 267 LEU cc_start: 0.8493 (mt) cc_final: 0.7996 (mt) REVERT: D 453 LYS cc_start: 0.8182 (mttt) cc_final: 0.7941 (tmtt) REVERT: D 473 PHE cc_start: 0.8251 (m-80) cc_final: 0.7461 (m-80) REVERT: D 479 LEU cc_start: 0.8280 (mt) cc_final: 0.7865 (mt) REVERT: D 487 LYS cc_start: 0.6940 (mttt) cc_final: 0.6657 (mmmt) REVERT: D 509 VAL cc_start: 0.7606 (t) cc_final: 0.7145 (t) REVERT: D 562 MET cc_start: 0.9300 (mmm) cc_final: 0.9095 (mtt) REVERT: D 606 TRP cc_start: 0.7324 (m100) cc_final: 0.6966 (m100) REVERT: D 653 MET cc_start: 0.5856 (mmm) cc_final: 0.5564 (mmp) REVERT: D 702 HIS cc_start: 0.9032 (m-70) cc_final: 0.8820 (m-70) REVERT: D 771 TRP cc_start: 0.8227 (m100) cc_final: 0.7806 (m100) REVERT: D 782 PHE cc_start: 0.8922 (m-80) cc_final: 0.8688 (m-80) REVERT: D 783 VAL cc_start: 0.9187 (t) cc_final: 0.8946 (t) REVERT: D 795 TRP cc_start: 0.9273 (m100) cc_final: 0.8762 (m100) REVERT: A 44 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8283 (mp0) REVERT: A 197 PHE cc_start: 0.7739 (m-80) cc_final: 0.7461 (m-80) REVERT: A 354 MET cc_start: 0.8361 (mmm) cc_final: 0.7980 (tpt) REVERT: A 358 ASN cc_start: 0.8841 (m-40) cc_final: 0.8537 (m-40) REVERT: A 472 PHE cc_start: 0.7597 (m-80) cc_final: 0.7326 (m-80) REVERT: A 555 MET cc_start: 0.8463 (mmm) cc_final: 0.8256 (mmp) REVERT: A 563 TRP cc_start: 0.7416 (m100) cc_final: 0.6505 (m100) REVERT: A 611 TRP cc_start: 0.7628 (m100) cc_final: 0.6962 (m100) REVERT: A 639 PHE cc_start: 0.8256 (m-80) cc_final: 0.7680 (m-80) REVERT: A 683 THR cc_start: 0.8743 (p) cc_final: 0.8487 (p) REVERT: A 706 MET cc_start: 0.9437 (mmm) cc_final: 0.9047 (mmm) REVERT: A 707 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8200 (mp0) REVERT: A 752 LEU cc_start: 0.8100 (mt) cc_final: 0.7094 (mm) REVERT: A 786 GLU cc_start: 0.8787 (mt-10) cc_final: 0.7934 (tp30) REVERT: A 789 ASP cc_start: 0.9456 (m-30) cc_final: 0.9235 (t0) REVERT: B 48 GLU cc_start: 0.9221 (mt-10) cc_final: 0.9019 (pm20) REVERT: B 80 LYS cc_start: 0.9033 (mttt) cc_final: 0.8814 (mttp) REVERT: B 102 ASP cc_start: 0.9261 (m-30) cc_final: 0.8989 (t0) REVERT: B 109 VAL cc_start: 0.8056 (t) cc_final: 0.7746 (m) REVERT: B 112 MET cc_start: 0.8398 (mmm) cc_final: 0.8105 (mmm) REVERT: B 122 VAL cc_start: 0.8760 (t) cc_final: 0.8337 (t) REVERT: B 125 LEU cc_start: 0.7769 (mt) cc_final: 0.7127 (mp) REVERT: B 134 ILE cc_start: 0.6640 (mt) cc_final: 0.5720 (mt) REVERT: B 135 MET cc_start: 0.7720 (mmm) cc_final: 0.7222 (mmm) REVERT: B 158 MET cc_start: 0.8838 (mmm) cc_final: 0.7861 (tpt) REVERT: B 159 LEU cc_start: 0.9541 (mt) cc_final: 0.9231 (mm) REVERT: B 161 ILE cc_start: 0.9639 (mt) cc_final: 0.9167 (mt) REVERT: B 169 VAL cc_start: 0.8691 (t) cc_final: 0.8438 (p) REVERT: B 192 ASP cc_start: 0.9344 (m-30) cc_final: 0.9110 (p0) REVERT: B 198 TRP cc_start: 0.7056 (m100) cc_final: 0.6008 (m100) REVERT: B 264 ASN cc_start: 0.9154 (m-40) cc_final: 0.8816 (p0) REVERT: B 267 LEU cc_start: 0.8709 (mt) cc_final: 0.7713 (mp) REVERT: B 334 LEU cc_start: 0.9522 (mt) cc_final: 0.8891 (mm) REVERT: B 338 MET cc_start: 0.8763 (mmm) cc_final: 0.8335 (mmm) REVERT: B 353 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8378 (mp0) REVERT: B 385 LEU cc_start: 0.8780 (mt) cc_final: 0.8320 (mm) REVERT: B 405 HIS cc_start: 0.7812 (m-70) cc_final: 0.7580 (m170) REVERT: B 473 PHE cc_start: 0.8400 (m-80) cc_final: 0.7848 (m-80) REVERT: B 496 MET cc_start: 0.7896 (mmm) cc_final: 0.6658 (mmm) REVERT: B 672 ARG cc_start: 0.9328 (mtt180) cc_final: 0.9034 (mmm160) REVERT: B 700 TYR cc_start: 0.9324 (m-80) cc_final: 0.8885 (p90) REVERT: B 707 LYS cc_start: 0.9441 (mttt) cc_final: 0.9232 (mtmm) REVERT: B 792 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8484 (mt-10) REVERT: B 794 LEU cc_start: 0.8269 (mt) cc_final: 0.7869 (mt) REVERT: B 839 HIS cc_start: 0.7824 (m-70) cc_final: 0.7446 (p-80) REVERT: C 37 LYS cc_start: 0.8945 (mttt) cc_final: 0.8416 (ptpp) REVERT: C 40 GLN cc_start: 0.9426 (mt0) cc_final: 0.9087 (mt0) REVERT: C 44 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8698 (mm-30) REVERT: C 91 LEU cc_start: 0.9156 (mt) cc_final: 0.8830 (mt) REVERT: C 147 GLN cc_start: 0.9331 (mt0) cc_final: 0.8703 (mp10) REVERT: C 166 LEU cc_start: 0.9085 (mt) cc_final: 0.8783 (mt) REVERT: C 172 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8519 (mt-10) REVERT: C 184 LEU cc_start: 0.9689 (mt) cc_final: 0.9468 (mm) REVERT: C 197 PHE cc_start: 0.8442 (m-80) cc_final: 0.7996 (m-80) REVERT: C 219 ILE cc_start: 0.8585 (mt) cc_final: 0.8362 (mp) REVERT: C 324 VAL cc_start: 0.9506 (t) cc_final: 0.9305 (m) REVERT: C 397 ARG cc_start: 0.9132 (mtt180) cc_final: 0.8549 (mmp80) REVERT: C 470 MET cc_start: 0.8467 (mmm) cc_final: 0.7947 (mmm) REVERT: C 517 LEU cc_start: 0.8836 (mt) cc_final: 0.8533 (mt) REVERT: C 639 PHE cc_start: 0.8659 (m-80) cc_final: 0.8182 (m-80) REVERT: C 685 LYS cc_start: 0.9287 (mttt) cc_final: 0.9051 (mtmm) REVERT: C 708 LYS cc_start: 0.9554 (mttt) cc_final: 0.9286 (ptpp) REVERT: C 711 TYR cc_start: 0.8797 (m-80) cc_final: 0.8242 (m-80) REVERT: C 726 LEU cc_start: 0.8699 (mt) cc_final: 0.8363 (mt) REVERT: C 784 PHE cc_start: 0.8593 (m-80) cc_final: 0.8333 (m-10) REVERT: C 790 LYS cc_start: 0.9395 (mttt) cc_final: 0.9122 (pttp) REVERT: C 794 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7556 (tpp-160) outliers start: 3 outliers final: 1 residues processed: 1036 average time/residue: 0.1729 time to fit residues: 271.0131 Evaluate side-chains 654 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 653 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0370 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 HIS D 96 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN D 515 ASN D 674 HIS D 687 ASN A 38 HIS A 61 ASN A 86 GLN A 134 HIS A 171 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 449 HIS A 520 ASN A 559 GLN B 35 ASN B 42 HIS B 85 HIS B 96 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 387 HIS B 444 ASN B 515 ASN B 697 ASN B 774 GLN C 38 HIS C 61 ASN C 73 GLN ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 161 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 375 ASN C 440 ASN C 449 HIS C 521 ASN C 536 GLN C 559 GLN ** C 709 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.112999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.084906 restraints weight = 183183.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089579 restraints weight = 95082.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092985 restraints weight = 60516.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095506 restraints weight = 42786.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.097384 restraints weight = 32508.267| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24452 Z= 0.178 Angle : 0.834 15.082 33152 Z= 0.449 Chirality : 0.053 0.381 3790 Planarity : 0.005 0.059 4182 Dihedral : 7.759 36.914 3280 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.64 % Favored : 92.10 % Rotamer: Outliers : 0.04 % Allowed : 2.04 % Favored : 97.92 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.10 % 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: -2.79 (0.14), residues: 3028 helix: -1.36 (0.13), residues: 1234 sheet: -0.93 (0.27), residues: 338 loop : -2.52 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 260 TYR 0.066 0.003 TYR C 232 PHE 0.046 0.002 PHE D 580 TRP 0.041 0.003 TRP D 255 HIS 0.014 0.002 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00377 (24442) covalent geometry : angle 0.82740 (33132) SS BOND : bond 0.00831 ( 10) SS BOND : angle 4.30091 ( 20) hydrogen bonds : bond 0.05202 ( 1019) hydrogen bonds : angle 6.95986 ( 2959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 803 time to evaluate : 1.023 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: 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: 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: D 38 VAL cc_start: 0.8411 (t) cc_final: 0.8069 (t) REVERT: D 39 MET cc_start: 0.7491 (mmp) cc_final: 0.7112 (mmp) REVERT: D 80 LYS cc_start: 0.9125 (mttt) cc_final: 0.8820 (mttt) REVERT: D 127 ILE cc_start: 0.8843 (mt) cc_final: 0.8601 (mm) REVERT: D 150 SER cc_start: 0.8364 (p) cc_final: 0.8079 (t) REVERT: D 160 LYS cc_start: 0.8312 (mttt) cc_final: 0.7515 (tttt) REVERT: D 264 ASN cc_start: 0.8940 (p0) cc_final: 0.8580 (p0) REVERT: D 448 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8572 (mp0) REVERT: D 473 PHE cc_start: 0.8082 (m-80) cc_final: 0.7184 (m-80) REVERT: D 515 ASN cc_start: 0.7388 (m110) cc_final: 0.6997 (m-40) REVERT: D 520 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8199 (mt-10) REVERT: D 524 PHE cc_start: 0.6401 (m-80) cc_final: 0.6161 (m-80) REVERT: D 562 MET cc_start: 0.9370 (mmm) cc_final: 0.9116 (mtt) REVERT: D 606 TRP cc_start: 0.7194 (m100) cc_final: 0.6663 (m100) REVERT: D 608 LEU cc_start: 0.8916 (mt) cc_final: 0.8675 (mt) REVERT: D 756 PHE cc_start: 0.8712 (m-80) cc_final: 0.8374 (m-10) REVERT: D 774 GLN cc_start: 0.9055 (mp10) cc_final: 0.8225 (mp10) REVERT: D 782 PHE cc_start: 0.8790 (m-80) cc_final: 0.8587 (m-80) REVERT: A 39 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9038 (mp0) REVERT: A 183 LEU cc_start: 0.8607 (mt) cc_final: 0.8374 (tp) REVERT: A 225 GLU cc_start: 0.7696 (tt0) cc_final: 0.7066 (tp30) REVERT: A 358 ASN cc_start: 0.8916 (m-40) cc_final: 0.8591 (m-40) REVERT: A 382 PRO cc_start: 0.7886 (Cg_endo) cc_final: 0.7679 (Cg_exo) REVERT: A 472 PHE cc_start: 0.7739 (m-80) cc_final: 0.7391 (m-80) REVERT: A 489 ARG cc_start: 0.6630 (mtt-85) cc_final: 0.5149 (mmt90) REVERT: A 502 MET cc_start: 0.8594 (mtt) cc_final: 0.8222 (mtp) REVERT: A 555 MET cc_start: 0.8507 (mmm) cc_final: 0.7996 (mmp) REVERT: A 563 TRP cc_start: 0.7607 (m100) cc_final: 0.7260 (m100) REVERT: A 611 TRP cc_start: 0.7447 (m100) cc_final: 0.7134 (m100) REVERT: A 639 PHE cc_start: 0.7931 (m-80) cc_final: 0.7490 (m-80) REVERT: A 663 ARG cc_start: 0.8270 (mtt180) cc_final: 0.7951 (ptt-90) REVERT: A 736 LEU cc_start: 0.8017 (tp) cc_final: 0.7634 (tp) REVERT: A 786 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8183 (tp30) REVERT: A 789 ASP cc_start: 0.9388 (m-30) cc_final: 0.9125 (t0) REVERT: B 80 LYS cc_start: 0.9079 (mttt) cc_final: 0.8803 (mttp) REVERT: B 102 ASP cc_start: 0.9297 (m-30) cc_final: 0.8950 (t0) REVERT: B 112 MET cc_start: 0.8470 (mmm) cc_final: 0.8250 (mmm) REVERT: B 134 ILE cc_start: 0.6855 (mt) cc_final: 0.6480 (mt) REVERT: B 135 MET cc_start: 0.7435 (mmm) cc_final: 0.7082 (mmm) REVERT: B 152 GLN cc_start: 0.9123 (pm20) cc_final: 0.8824 (pm20) REVERT: B 153 GLN cc_start: 0.9562 (mp10) cc_final: 0.9268 (mm110) REVERT: B 161 ILE cc_start: 0.9500 (mt) cc_final: 0.9244 (mt) REVERT: B 167 TRP cc_start: 0.7279 (m100) cc_final: 0.6980 (m100) REVERT: B 192 ASP cc_start: 0.9077 (m-30) cc_final: 0.8873 (m-30) REVERT: B 227 ILE cc_start: 0.8606 (mt) cc_final: 0.8388 (mt) REVERT: B 309 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8882 (tptp) REVERT: B 334 LEU cc_start: 0.9550 (mt) cc_final: 0.9068 (mm) REVERT: B 338 MET cc_start: 0.8696 (mmm) cc_final: 0.8451 (mmm) REVERT: B 355 TYR cc_start: 0.8901 (m-80) cc_final: 0.8594 (m-80) REVERT: B 385 LEU cc_start: 0.8971 (mt) cc_final: 0.8738 (mt) REVERT: B 405 HIS cc_start: 0.7831 (m-70) cc_final: 0.7489 (m170) REVERT: B 437 ARG cc_start: 0.5471 (mtt180) cc_final: 0.3214 (ttm-80) REVERT: B 473 PHE cc_start: 0.8068 (m-80) cc_final: 0.7641 (m-80) REVERT: B 478 TYR cc_start: 0.7887 (m-10) cc_final: 0.7157 (m-10) REVERT: B 496 MET cc_start: 0.8178 (mmm) cc_final: 0.7781 (mmm) REVERT: B 501 VAL cc_start: 0.9029 (t) cc_final: 0.8776 (p) REVERT: B 562 MET cc_start: 0.9398 (mpp) cc_final: 0.9192 (mpp) REVERT: B 565 MET cc_start: 0.8731 (ppp) cc_final: 0.8357 (ppp) REVERT: B 696 ASN cc_start: 0.8989 (m-40) cc_final: 0.8693 (m110) REVERT: B 700 TYR cc_start: 0.9241 (m-80) cc_final: 0.8771 (t80) REVERT: B 707 LYS cc_start: 0.9455 (mttt) cc_final: 0.9244 (mtmm) REVERT: B 781 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8335 (tp-100) REVERT: B 787 GLU cc_start: 0.9547 (mt-10) cc_final: 0.9106 (mp0) REVERT: B 792 GLU cc_start: 0.9201 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 833 ILE cc_start: 0.8643 (tt) cc_final: 0.8422 (tt) REVERT: B 837 TRP cc_start: 0.7934 (m100) cc_final: 0.7475 (m100) REVERT: C 39 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8241 (mp0) REVERT: C 44 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8864 (mm-30) REVERT: C 147 GLN cc_start: 0.9326 (mt0) cc_final: 0.8756 (mp10) REVERT: C 166 LEU cc_start: 0.9253 (mt) cc_final: 0.8829 (mt) REVERT: C 171 HIS cc_start: 0.8450 (t70) cc_final: 0.7904 (t70) REVERT: C 172 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8298 (mt-10) REVERT: C 197 PHE cc_start: 0.8173 (m-80) cc_final: 0.7786 (m-80) REVERT: C 214 LEU cc_start: 0.8634 (mt) cc_final: 0.8256 (mt) REVERT: C 281 ILE cc_start: 0.9372 (mt) cc_final: 0.9143 (mt) REVERT: C 341 ASN cc_start: 0.8057 (m-40) cc_final: 0.7709 (m-40) REVERT: C 359 ARG cc_start: 0.9410 (mtt180) cc_final: 0.9073 (mmm-85) REVERT: C 434 VAL cc_start: 0.8495 (t) cc_final: 0.8054 (m) REVERT: C 470 MET cc_start: 0.8384 (mmm) cc_final: 0.7949 (mmm) REVERT: C 475 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7903 (mp0) REVERT: C 477 HIS cc_start: 0.8463 (m90) cc_final: 0.8130 (m90) REVERT: C 520 ASN cc_start: 0.7667 (m110) cc_final: 0.7343 (m-40) REVERT: C 576 MET cc_start: 0.8446 (ptt) cc_final: 0.7882 (ptt) REVERT: C 636 TRP cc_start: 0.7918 (m100) cc_final: 0.7643 (m100) REVERT: C 689 VAL cc_start: 0.9110 (t) cc_final: 0.8697 (p) REVERT: C 690 ASP cc_start: 0.9108 (m-30) cc_final: 0.8840 (m-30) REVERT: C 694 ARG cc_start: 0.9110 (mtt180) cc_final: 0.8685 (ttm170) REVERT: C 708 LYS cc_start: 0.9473 (mttt) cc_final: 0.9221 (ptpp) REVERT: C 737 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9077 (mm-30) REVERT: C 786 GLU cc_start: 0.9328 (tp30) cc_final: 0.8889 (tp30) outliers start: 1 outliers final: 0 residues processed: 804 average time/residue: 0.1643 time to fit residues: 203.6393 Evaluate side-chains 624 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 139 optimal weight: 0.9990 chunk 296 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 153 optimal weight: 30.0000 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 256 optimal weight: 0.4980 chunk 274 optimal weight: 20.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 HIS D 494 ASN D 687 ASN D 816 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN A 571 HIS A 812 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.112293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084244 restraints weight = 190308.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088814 restraints weight = 98222.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.092150 restraints weight = 62415.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094651 restraints weight = 44119.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096500 restraints weight = 33543.271| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24452 Z= 0.155 Angle : 0.756 13.772 33152 Z= 0.400 Chirality : 0.049 0.284 3790 Planarity : 0.005 0.065 4182 Dihedral : 7.058 34.548 3280 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.20 % Favored : 91.53 % Rotamer: Outliers : 0.04 % Allowed : 1.85 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.10 % 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: -2.31 (0.14), residues: 3028 helix: -0.87 (0.14), residues: 1254 sheet: -1.04 (0.26), residues: 352 loop : -2.27 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 763 TYR 0.049 0.003 TYR C 232 PHE 0.037 0.002 PHE B 459 TRP 0.067 0.003 TRP A 636 HIS 0.010 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00334 (24442) covalent geometry : angle 0.75121 (33132) SS BOND : bond 0.00491 ( 10) SS BOND : angle 3.51389 ( 20) hydrogen bonds : bond 0.04661 ( 1019) hydrogen bonds : angle 6.51387 ( 2959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 733 time to evaluate : 0.862 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: 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: 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: D 38 VAL cc_start: 0.8629 (t) cc_final: 0.8364 (t) REVERT: D 39 MET cc_start: 0.7705 (mmp) cc_final: 0.7328 (mmp) REVERT: D 150 SER cc_start: 0.8408 (p) cc_final: 0.6583 (t) REVERT: D 151 ILE cc_start: 0.8377 (tt) cc_final: 0.8075 (tt) REVERT: D 160 LYS cc_start: 0.8080 (mttt) cc_final: 0.7300 (tttp) REVERT: D 182 GLU cc_start: 0.9312 (mp0) cc_final: 0.8986 (mp0) REVERT: D 198 TRP cc_start: 0.7390 (m100) cc_final: 0.6631 (m100) REVERT: D 199 ASP cc_start: 0.8421 (m-30) cc_final: 0.8132 (t0) REVERT: D 264 ASN cc_start: 0.9152 (p0) cc_final: 0.8701 (p0) REVERT: D 334 LEU cc_start: 0.9456 (mm) cc_final: 0.8999 (mm) REVERT: D 448 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8534 (mp0) REVERT: D 459 PHE cc_start: 0.7308 (m-80) cc_final: 0.6231 (m-80) REVERT: D 476 ASP cc_start: 0.8701 (m-30) cc_final: 0.8415 (p0) REVERT: D 496 MET cc_start: 0.8442 (mmt) cc_final: 0.7966 (mtm) REVERT: D 512 LEU cc_start: 0.8143 (mt) cc_final: 0.7547 (mt) REVERT: D 524 PHE cc_start: 0.6239 (m-80) cc_final: 0.5983 (m-10) REVERT: D 606 TRP cc_start: 0.7439 (m100) cc_final: 0.6894 (m100) REVERT: D 608 LEU cc_start: 0.8866 (mt) cc_final: 0.8575 (mt) REVERT: D 774 GLN cc_start: 0.8992 (mp10) cc_final: 0.8616 (mp10) REVERT: D 788 MET cc_start: 0.9238 (mtm) cc_final: 0.8948 (mtm) REVERT: A 39 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9079 (mp0) REVERT: A 125 MET cc_start: 0.8033 (mmp) cc_final: 0.7414 (mmm) REVERT: A 183 LEU cc_start: 0.8553 (mt) cc_final: 0.8339 (tp) REVERT: A 209 MET cc_start: 0.9535 (tpt) cc_final: 0.9331 (tpp) REVERT: A 225 GLU cc_start: 0.7724 (tt0) cc_final: 0.7209 (tp30) REVERT: A 358 ASN cc_start: 0.9017 (m-40) cc_final: 0.8775 (m-40) REVERT: A 378 LYS cc_start: 0.8956 (mttt) cc_final: 0.8691 (tptm) REVERT: A 458 PHE cc_start: 0.8286 (m-80) cc_final: 0.7898 (m-80) REVERT: A 472 PHE cc_start: 0.8063 (m-80) cc_final: 0.7605 (m-80) REVERT: A 489 ARG cc_start: 0.6202 (mtt-85) cc_final: 0.5797 (mmt90) REVERT: A 555 MET cc_start: 0.8121 (mmm) cc_final: 0.7582 (mmp) REVERT: A 563 TRP cc_start: 0.7793 (m100) cc_final: 0.7315 (m100) REVERT: A 611 TRP cc_start: 0.7549 (m100) cc_final: 0.7173 (m100) REVERT: A 663 ARG cc_start: 0.8447 (mtt180) cc_final: 0.7845 (pmt-80) REVERT: A 707 GLU cc_start: 0.8401 (mp0) cc_final: 0.8187 (mp0) REVERT: A 736 LEU cc_start: 0.7887 (tp) cc_final: 0.7394 (tp) REVERT: A 737 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8127 (mm-30) REVERT: A 769 LYS cc_start: 0.9338 (ptmm) cc_final: 0.9118 (pptt) REVERT: B 80 LYS cc_start: 0.9073 (mttt) cc_final: 0.8790 (mttp) REVERT: B 84 THR cc_start: 0.9195 (t) cc_final: 0.8852 (t) REVERT: B 85 HIS cc_start: 0.8884 (m90) cc_final: 0.8590 (m90) REVERT: B 102 ASP cc_start: 0.9340 (m-30) cc_final: 0.8893 (t0) REVERT: B 112 MET cc_start: 0.8624 (mmm) cc_final: 0.8402 (mmm) REVERT: B 134 ILE cc_start: 0.6788 (mt) cc_final: 0.5949 (mt) REVERT: B 135 MET cc_start: 0.7397 (mmm) cc_final: 0.7108 (mmm) REVERT: B 152 GLN cc_start: 0.9151 (pm20) cc_final: 0.8785 (pm20) REVERT: B 153 GLN cc_start: 0.9502 (mp10) cc_final: 0.9192 (mp10) REVERT: B 158 MET cc_start: 0.9012 (mtt) cc_final: 0.8762 (mtt) REVERT: B 167 TRP cc_start: 0.7641 (m100) cc_final: 0.7366 (m100) REVERT: B 227 ILE cc_start: 0.8706 (mt) cc_final: 0.8505 (mt) REVERT: B 255 TRP cc_start: 0.8756 (m100) cc_final: 0.8347 (m-10) REVERT: B 334 LEU cc_start: 0.9504 (mt) cc_final: 0.8878 (mm) REVERT: B 338 MET cc_start: 0.8714 (mmm) cc_final: 0.8407 (mmm) REVERT: B 355 TYR cc_start: 0.8945 (m-80) cc_final: 0.8628 (m-80) REVERT: B 405 HIS cc_start: 0.7870 (m-70) cc_final: 0.7438 (m170) REVERT: B 455 CYS cc_start: 0.8343 (m) cc_final: 0.6822 (m) REVERT: B 473 PHE cc_start: 0.8152 (m-80) cc_final: 0.7666 (m-80) REVERT: B 507 MET cc_start: 0.9027 (tpp) cc_final: 0.8740 (tpp) REVERT: B 696 ASN cc_start: 0.8967 (m-40) cc_final: 0.8636 (m110) REVERT: B 700 TYR cc_start: 0.9269 (m-80) cc_final: 0.8849 (p90) REVERT: B 707 LYS cc_start: 0.9485 (mttt) cc_final: 0.9265 (mtmm) REVERT: B 787 GLU cc_start: 0.9418 (mt-10) cc_final: 0.8738 (pt0) REVERT: B 790 GLU cc_start: 0.9442 (tp30) cc_final: 0.8914 (tp30) REVERT: B 792 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8742 (mt-10) REVERT: B 794 LEU cc_start: 0.8356 (mt) cc_final: 0.7618 (mt) REVERT: B 839 HIS cc_start: 0.8524 (p-80) cc_final: 0.8319 (p-80) REVERT: C 39 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8320 (mp0) REVERT: C 166 LEU cc_start: 0.9233 (mt) cc_final: 0.8895 (mt) REVERT: C 171 HIS cc_start: 0.8438 (t70) cc_final: 0.7863 (t70) REVERT: C 172 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8096 (mt-10) REVERT: C 177 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8454 (tp-100) REVERT: C 209 MET cc_start: 0.8970 (tpt) cc_final: 0.8483 (ptp) REVERT: C 240 MET cc_start: 0.7315 (mpp) cc_final: 0.6770 (mpp) REVERT: C 245 TYR cc_start: 0.7375 (m-80) cc_final: 0.6472 (m-10) REVERT: C 359 ARG cc_start: 0.9457 (mtt180) cc_final: 0.9011 (mmm-85) REVERT: C 392 TYR cc_start: 0.6792 (m-80) cc_final: 0.6395 (m-80) REVERT: C 397 ARG cc_start: 0.9032 (mtt180) cc_final: 0.8776 (mmt90) REVERT: C 470 MET cc_start: 0.8528 (mmm) cc_final: 0.8067 (mmm) REVERT: C 501 MET cc_start: 0.9281 (ptp) cc_final: 0.9058 (mpp) REVERT: C 502 MET cc_start: 0.8466 (mpp) cc_final: 0.8162 (mpp) REVERT: C 512 MET cc_start: 0.7456 (tpt) cc_final: 0.7124 (tpp) REVERT: C 525 GLN cc_start: 0.9155 (mt0) cc_final: 0.8897 (mt0) REVERT: C 539 THR cc_start: 0.9003 (m) cc_final: 0.8543 (p) REVERT: C 576 MET cc_start: 0.8514 (ptt) cc_final: 0.8078 (ptm) REVERT: C 635 VAL cc_start: 0.8794 (t) cc_final: 0.8588 (t) REVERT: C 636 TRP cc_start: 0.8068 (m100) cc_final: 0.7789 (m100) REVERT: C 641 MET cc_start: 0.9475 (tmm) cc_final: 0.9076 (ttm) REVERT: C 689 VAL cc_start: 0.9155 (t) cc_final: 0.8846 (p) REVERT: C 690 ASP cc_start: 0.9135 (m-30) cc_final: 0.8886 (m-30) REVERT: C 694 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8882 (ttm170) REVERT: C 708 LYS cc_start: 0.9543 (mttt) cc_final: 0.9280 (ptpp) REVERT: C 731 TRP cc_start: 0.9149 (t-100) cc_final: 0.8929 (t-100) REVERT: C 736 LEU cc_start: 0.8962 (mt) cc_final: 0.8652 (mt) REVERT: C 739 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8633 (mm-30) REVERT: C 786 GLU cc_start: 0.9452 (tp30) cc_final: 0.9068 (tp30) REVERT: C 789 ASP cc_start: 0.9447 (t70) cc_final: 0.8965 (t0) REVERT: C 790 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8776 (mmmt) outliers start: 1 outliers final: 0 residues processed: 734 average time/residue: 0.1571 time to fit residues: 180.9011 Evaluate side-chains 598 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 597 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 136 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 58 optimal weight: 0.0040 chunk 133 optimal weight: 7.9990 chunk 16 optimal weight: 0.0470 chunk 67 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 204 optimal weight: 30.0000 chunk 62 optimal weight: 0.0030 chunk 291 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 375 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.111402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084287 restraints weight = 161716.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.088537 restraints weight = 90578.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.091675 restraints weight = 60028.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093983 restraints weight = 43633.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095756 restraints weight = 33810.534| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24452 Z= 0.144 Angle : 0.727 11.866 33152 Z= 0.384 Chirality : 0.049 0.283 3790 Planarity : 0.004 0.064 4182 Dihedral : 6.667 34.069 3280 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.27 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.15), residues: 3028 helix: -0.53 (0.14), residues: 1248 sheet: -1.12 (0.26), residues: 356 loop : -2.13 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 377 TYR 0.048 0.002 TYR C 232 PHE 0.042 0.002 PHE A 639 TRP 0.068 0.003 TRP A 151 HIS 0.012 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00315 (24442) covalent geometry : angle 0.72321 (33132) SS BOND : bond 0.01039 ( 10) SS BOND : angle 3.16524 ( 20) hydrogen bonds : bond 0.04254 ( 1019) hydrogen bonds : angle 6.24546 ( 2959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 0.888 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: 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: D 38 VAL cc_start: 0.8625 (t) cc_final: 0.8385 (t) REVERT: D 39 MET cc_start: 0.7680 (mmp) cc_final: 0.7390 (mmp) REVERT: D 80 LYS cc_start: 0.9199 (mttt) cc_final: 0.8860 (mttp) REVERT: D 119 HIS cc_start: 0.8552 (m-70) cc_final: 0.8032 (m90) REVERT: D 160 LYS cc_start: 0.7970 (mttt) cc_final: 0.7272 (tttp) REVERT: D 182 GLU cc_start: 0.9353 (mp0) cc_final: 0.9122 (mp0) REVERT: D 198 TRP cc_start: 0.6829 (m100) cc_final: 0.6452 (m100) REVERT: D 199 ASP cc_start: 0.8571 (m-30) cc_final: 0.8283 (t0) REVERT: D 264 ASN cc_start: 0.9138 (p0) cc_final: 0.8686 (p0) REVERT: D 355 TYR cc_start: 0.8380 (m-80) cc_final: 0.7987 (m-80) REVERT: D 448 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8521 (mp0) REVERT: D 459 PHE cc_start: 0.7592 (m-80) cc_final: 0.6321 (m-80) REVERT: D 496 MET cc_start: 0.8480 (mmt) cc_final: 0.8013 (mtm) REVERT: D 499 GLU cc_start: 0.8611 (tp30) cc_final: 0.8337 (tp30) REVERT: D 507 MET cc_start: 0.7887 (tpt) cc_final: 0.7354 (tpt) REVERT: D 512 LEU cc_start: 0.8058 (mt) cc_final: 0.7331 (mt) REVERT: D 606 TRP cc_start: 0.7349 (m100) cc_final: 0.6838 (m100) REVERT: D 641 PHE cc_start: 0.8769 (m-80) cc_final: 0.8553 (m-80) REVERT: D 703 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8931 (tm-30) REVERT: D 774 GLN cc_start: 0.9077 (mp10) cc_final: 0.8662 (mp10) REVERT: D 788 MET cc_start: 0.9339 (mtm) cc_final: 0.8808 (mtm) REVERT: D 790 GLU cc_start: 0.9504 (mp0) cc_final: 0.9298 (mp0) REVERT: D 791 LEU cc_start: 0.8854 (tt) cc_final: 0.8633 (tt) REVERT: A 39 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8931 (mp0) REVERT: A 66 THR cc_start: 0.7997 (p) cc_final: 0.7784 (p) REVERT: A 183 LEU cc_start: 0.8579 (mt) cc_final: 0.8248 (mm) REVERT: A 187 ARG cc_start: 0.8064 (ptp-170) cc_final: 0.7835 (ptp-170) REVERT: A 209 MET cc_start: 0.9523 (tpt) cc_final: 0.9312 (tpp) REVERT: A 225 GLU cc_start: 0.7754 (tt0) cc_final: 0.7247 (tp30) REVERT: A 248 LEU cc_start: 0.9356 (tp) cc_final: 0.8807 (tp) REVERT: A 357 GLN cc_start: 0.8423 (mt0) cc_final: 0.7738 (pp30) REVERT: A 358 ASN cc_start: 0.9057 (m-40) cc_final: 0.8420 (m-40) REVERT: A 472 PHE cc_start: 0.8150 (m-80) cc_final: 0.7627 (m-80) REVERT: A 477 HIS cc_start: 0.8809 (t-90) cc_final: 0.8532 (t70) REVERT: A 533 PHE cc_start: 0.7505 (m-80) cc_final: 0.6589 (m-80) REVERT: A 534 LYS cc_start: 0.8457 (mppt) cc_final: 0.7932 (mtpp) REVERT: A 563 TRP cc_start: 0.7868 (m100) cc_final: 0.7556 (m100) REVERT: A 611 TRP cc_start: 0.7615 (m100) cc_final: 0.7282 (m100) REVERT: A 663 ARG cc_start: 0.8554 (mtt180) cc_final: 0.8010 (pmt-80) REVERT: A 736 LEU cc_start: 0.7875 (tp) cc_final: 0.7391 (tp) REVERT: A 737 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8246 (mm-30) REVERT: A 762 MET cc_start: 0.7467 (mmm) cc_final: 0.6676 (mtp) REVERT: B 80 LYS cc_start: 0.9068 (mttt) cc_final: 0.8735 (mtmm) REVERT: B 99 VAL cc_start: 0.8984 (t) cc_final: 0.8629 (t) REVERT: B 100 PHE cc_start: 0.8878 (m-80) cc_final: 0.7904 (m-80) REVERT: B 102 ASP cc_start: 0.9367 (m-30) cc_final: 0.8910 (t0) REVERT: B 134 ILE cc_start: 0.6921 (mt) cc_final: 0.6130 (mt) REVERT: B 135 MET cc_start: 0.7351 (mmm) cc_final: 0.7103 (mmm) REVERT: B 158 MET cc_start: 0.9170 (mtt) cc_final: 0.8540 (mtt) REVERT: B 159 LEU cc_start: 0.9590 (mt) cc_final: 0.9368 (mt) REVERT: B 167 TRP cc_start: 0.7473 (m100) cc_final: 0.7182 (m100) REVERT: B 182 GLU cc_start: 0.9674 (mt-10) cc_final: 0.9471 (mp0) REVERT: B 227 ILE cc_start: 0.8812 (mt) cc_final: 0.8555 (mt) REVERT: B 255 TRP cc_start: 0.8741 (m100) cc_final: 0.8309 (m-10) REVERT: B 257 VAL cc_start: 0.8780 (t) cc_final: 0.8505 (t) REVERT: B 264 ASN cc_start: 0.9101 (m-40) cc_final: 0.8814 (t0) REVERT: B 338 MET cc_start: 0.8727 (mmm) cc_final: 0.8504 (mmm) REVERT: B 343 TRP cc_start: 0.8124 (t-100) cc_final: 0.7853 (t-100) REVERT: B 355 TYR cc_start: 0.8941 (m-80) cc_final: 0.8699 (m-80) REVERT: B 405 HIS cc_start: 0.7796 (m-70) cc_final: 0.7370 (m170) REVERT: B 437 ARG cc_start: 0.4632 (mtt180) cc_final: 0.2900 (mtt180) REVERT: B 455 CYS cc_start: 0.7586 (m) cc_final: 0.6908 (m) REVERT: B 459 PHE cc_start: 0.8790 (m-80) cc_final: 0.8349 (m-80) REVERT: B 473 PHE cc_start: 0.8099 (m-80) cc_final: 0.7606 (m-80) REVERT: B 496 MET cc_start: 0.8220 (mmm) cc_final: 0.7068 (mmm) REVERT: B 499 GLU cc_start: 0.9139 (tp30) cc_final: 0.8882 (tp30) REVERT: B 696 ASN cc_start: 0.8910 (m-40) cc_final: 0.8539 (m110) REVERT: B 700 TYR cc_start: 0.9239 (m-80) cc_final: 0.8870 (p90) REVERT: B 781 GLN cc_start: 0.8618 (tp-100) cc_final: 0.8163 (tp-100) REVERT: B 787 GLU cc_start: 0.9446 (mt-10) cc_final: 0.8856 (mp0) REVERT: B 792 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8790 (mt-10) REVERT: B 839 HIS cc_start: 0.8574 (p-80) cc_final: 0.8290 (p-80) REVERT: C 42 PHE cc_start: 0.9005 (m-80) cc_final: 0.8534 (m-80) REVERT: C 70 ASN cc_start: 0.9124 (p0) cc_final: 0.8624 (p0) REVERT: C 166 LEU cc_start: 0.9205 (mt) cc_final: 0.8912 (mt) REVERT: C 171 HIS cc_start: 0.8445 (t70) cc_final: 0.7859 (t70) REVERT: C 172 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8063 (mt-10) REVERT: C 245 TYR cc_start: 0.8200 (m-80) cc_final: 0.7781 (m-80) REVERT: C 359 ARG cc_start: 0.9473 (mtt180) cc_final: 0.9030 (mmm-85) REVERT: C 434 VAL cc_start: 0.8509 (m) cc_final: 0.8103 (t) REVERT: C 470 MET cc_start: 0.8482 (mmm) cc_final: 0.8116 (mmm) REVERT: C 472 PHE cc_start: 0.8290 (m-80) cc_final: 0.8032 (m-80) REVERT: C 477 HIS cc_start: 0.8745 (m90) cc_final: 0.8485 (m90) REVERT: C 512 MET cc_start: 0.7191 (tpt) cc_final: 0.6823 (tpp) REVERT: C 539 THR cc_start: 0.9047 (m) cc_final: 0.8570 (p) REVERT: C 576 MET cc_start: 0.8709 (ptt) cc_final: 0.8368 (ptm) REVERT: C 635 VAL cc_start: 0.8903 (t) cc_final: 0.8703 (t) REVERT: C 636 TRP cc_start: 0.8044 (m100) cc_final: 0.7700 (m100) REVERT: C 641 MET cc_start: 0.9423 (tmm) cc_final: 0.9063 (ttm) REVERT: C 689 VAL cc_start: 0.9183 (t) cc_final: 0.8900 (p) REVERT: C 690 ASP cc_start: 0.9134 (m-30) cc_final: 0.8869 (m-30) REVERT: C 694 ARG cc_start: 0.9089 (mtt180) cc_final: 0.8882 (ttm170) REVERT: C 708 LYS cc_start: 0.9575 (mttt) cc_final: 0.9265 (ptpp) REVERT: C 731 TRP cc_start: 0.9127 (t-100) cc_final: 0.8893 (t-100) REVERT: C 736 LEU cc_start: 0.8957 (mt) cc_final: 0.8649 (mt) REVERT: C 786 GLU cc_start: 0.9433 (tp30) cc_final: 0.9074 (tp30) REVERT: C 789 ASP cc_start: 0.9422 (t70) cc_final: 0.9098 (t0) REVERT: C 790 LYS cc_start: 0.9177 (mmpt) cc_final: 0.8746 (mmmt) outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 0.1570 time to fit residues: 170.9234 Evaluate side-chains 586 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 110 optimal weight: 0.0270 chunk 279 optimal weight: 8.9990 chunk 274 optimal weight: 20.0000 chunk 92 optimal weight: 0.0770 chunk 162 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 overall best weight: 2.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN D 153 GLN D 697 ASN D 702 HIS A 94 HIS ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN A 719 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS C 710 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.084997 restraints weight = 175882.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.089489 restraints weight = 95828.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.092711 restraints weight = 62480.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095128 restraints weight = 44995.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.096977 restraints weight = 34590.904| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24452 Z= 0.139 Angle : 0.700 10.706 33152 Z= 0.370 Chirality : 0.048 0.249 3790 Planarity : 0.004 0.079 4182 Dihedral : 6.336 33.422 3280 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.10 % Favored : 91.63 % Rotamer: Outliers : 0.04 % Allowed : 1.06 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.15), residues: 3028 helix: -0.35 (0.14), residues: 1236 sheet: -0.98 (0.29), residues: 306 loop : -1.88 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 124 TYR 0.044 0.002 TYR C 232 PHE 0.037 0.002 PHE C 639 TRP 0.071 0.003 TRP A 636 HIS 0.013 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00301 (24442) covalent geometry : angle 0.69535 (33132) SS BOND : bond 0.00549 ( 10) SS BOND : angle 3.36133 ( 20) hydrogen bonds : bond 0.04184 ( 1019) hydrogen bonds : angle 6.05792 ( 2959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 682 time to evaluate : 0.891 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: 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: D 38 VAL cc_start: 0.8681 (t) cc_final: 0.8451 (t) REVERT: D 39 MET cc_start: 0.7749 (mmp) cc_final: 0.7407 (mmp) REVERT: D 80 LYS cc_start: 0.9246 (mttt) cc_final: 0.8984 (mtmt) REVERT: D 119 HIS cc_start: 0.8671 (m-70) cc_final: 0.8141 (m90) REVERT: D 264 ASN cc_start: 0.9144 (p0) cc_final: 0.8783 (p0) REVERT: D 343 TRP cc_start: 0.7284 (t60) cc_final: 0.6945 (t60) REVERT: D 355 TYR cc_start: 0.8669 (m-80) cc_final: 0.7941 (m-80) REVERT: D 437 ARG cc_start: 0.5038 (mtt180) cc_final: 0.4548 (mtt180) REVERT: D 448 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8499 (mp0) REVERT: D 459 PHE cc_start: 0.7604 (m-80) cc_final: 0.6329 (m-80) REVERT: D 499 GLU cc_start: 0.8655 (tp30) cc_final: 0.8367 (tp30) REVERT: D 507 MET cc_start: 0.7979 (tpt) cc_final: 0.7326 (tpt) REVERT: D 512 LEU cc_start: 0.8006 (mt) cc_final: 0.7592 (mt) REVERT: D 518 ARG cc_start: 0.8569 (mtt-85) cc_final: 0.7873 (mtt-85) REVERT: D 534 SER cc_start: 0.9221 (p) cc_final: 0.8751 (p) REVERT: D 606 TRP cc_start: 0.7560 (m100) cc_final: 0.6750 (m100) REVERT: D 774 GLN cc_start: 0.9096 (mp10) cc_final: 0.8670 (mp10) REVERT: D 788 MET cc_start: 0.9347 (mtm) cc_final: 0.8953 (mtm) REVERT: D 790 GLU cc_start: 0.9533 (mp0) cc_final: 0.9327 (mp0) REVERT: D 791 LEU cc_start: 0.8934 (tt) cc_final: 0.8657 (tp) REVERT: A 39 GLU cc_start: 0.9367 (mt-10) cc_final: 0.9053 (mp0) REVERT: A 183 LEU cc_start: 0.8572 (mt) cc_final: 0.8267 (tp) REVERT: A 209 MET cc_start: 0.9467 (tpt) cc_final: 0.9161 (tpp) REVERT: A 225 GLU cc_start: 0.7748 (tt0) cc_final: 0.7270 (tp30) REVERT: A 248 LEU cc_start: 0.9343 (tp) cc_final: 0.8881 (tp) REVERT: A 252 ARG cc_start: 0.8502 (ptp90) cc_final: 0.8100 (ptp90) REVERT: A 357 GLN cc_start: 0.8467 (mt0) cc_final: 0.7870 (pp30) REVERT: A 358 ASN cc_start: 0.9072 (m-40) cc_final: 0.8362 (m-40) REVERT: A 458 PHE cc_start: 0.8523 (m-80) cc_final: 0.8245 (m-80) REVERT: A 472 PHE cc_start: 0.8306 (m-80) cc_final: 0.7776 (m-80) REVERT: A 477 HIS cc_start: 0.8786 (t-90) cc_final: 0.8558 (t70) REVERT: A 489 ARG cc_start: 0.5484 (mmt90) cc_final: 0.5013 (tpp-160) REVERT: A 533 PHE cc_start: 0.7542 (m-80) cc_final: 0.6601 (m-80) REVERT: A 534 LYS cc_start: 0.8459 (mppt) cc_final: 0.8079 (mtpp) REVERT: A 563 TRP cc_start: 0.7872 (m100) cc_final: 0.7586 (m100) REVERT: A 611 TRP cc_start: 0.7688 (m100) cc_final: 0.7355 (m100) REVERT: A 663 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8087 (pmt-80) REVERT: A 698 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9217 (tm-30) REVERT: A 736 LEU cc_start: 0.7991 (tp) cc_final: 0.7532 (tp) REVERT: A 737 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8324 (mm-30) REVERT: A 762 MET cc_start: 0.7651 (mmm) cc_final: 0.6697 (mtp) REVERT: B 102 ASP cc_start: 0.9368 (m-30) cc_final: 0.8834 (t0) REVERT: B 112 MET cc_start: 0.8468 (mmm) cc_final: 0.8255 (mmm) REVERT: B 134 ILE cc_start: 0.7225 (mt) cc_final: 0.6122 (mt) REVERT: B 158 MET cc_start: 0.9350 (mtt) cc_final: 0.8732 (mtt) REVERT: B 159 LEU cc_start: 0.9628 (mt) cc_final: 0.9407 (mt) REVERT: B 167 TRP cc_start: 0.7557 (m100) cc_final: 0.7247 (m100) REVERT: B 182 GLU cc_start: 0.9654 (mt-10) cc_final: 0.9448 (mp0) REVERT: B 227 ILE cc_start: 0.8892 (mt) cc_final: 0.8631 (mt) REVERT: B 251 TYR cc_start: 0.4559 (m-80) cc_final: 0.3847 (m-80) REVERT: B 255 TRP cc_start: 0.8766 (m100) cc_final: 0.8325 (m-10) REVERT: B 264 ASN cc_start: 0.9153 (m-40) cc_final: 0.8903 (t0) REVERT: B 285 ASP cc_start: 0.9034 (p0) cc_final: 0.8821 (p0) REVERT: B 334 LEU cc_start: 0.9532 (mt) cc_final: 0.8897 (mt) REVERT: B 338 MET cc_start: 0.8826 (mmm) cc_final: 0.8550 (mmm) REVERT: B 355 TYR cc_start: 0.9032 (m-80) cc_final: 0.8062 (m-80) REVERT: B 385 LEU cc_start: 0.9008 (mt) cc_final: 0.8797 (mt) REVERT: B 405 HIS cc_start: 0.7887 (m-70) cc_final: 0.7463 (m170) REVERT: B 437 ARG cc_start: 0.4538 (mtt180) cc_final: 0.2821 (mtt180) REVERT: B 473 PHE cc_start: 0.8130 (m-80) cc_final: 0.7611 (m-80) REVERT: B 496 MET cc_start: 0.8204 (mmm) cc_final: 0.7162 (mmm) REVERT: B 507 MET cc_start: 0.8996 (tpp) cc_final: 0.8699 (tpp) REVERT: B 696 ASN cc_start: 0.8887 (m-40) cc_final: 0.8544 (m-40) REVERT: B 700 TYR cc_start: 0.9268 (m-80) cc_final: 0.8809 (p90) REVERT: B 781 GLN cc_start: 0.8604 (tp-100) cc_final: 0.8139 (tp-100) REVERT: B 787 GLU cc_start: 0.9438 (mt-10) cc_final: 0.8792 (mp0) REVERT: B 790 GLU cc_start: 0.9408 (tp30) cc_final: 0.8905 (tp30) REVERT: B 792 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 794 LEU cc_start: 0.8322 (mt) cc_final: 0.7595 (mt) REVERT: B 839 HIS cc_start: 0.8581 (p-80) cc_final: 0.8322 (p-80) REVERT: C 42 PHE cc_start: 0.8985 (m-80) cc_final: 0.8465 (m-80) REVERT: C 70 ASN cc_start: 0.8982 (p0) cc_final: 0.8640 (p0) REVERT: C 171 HIS cc_start: 0.8354 (t70) cc_final: 0.7873 (t70) REVERT: C 172 GLU cc_start: 0.8426 (mt-10) cc_final: 0.7837 (pp20) REVERT: C 198 ASP cc_start: 0.8945 (m-30) cc_final: 0.8718 (t0) REVERT: C 240 MET cc_start: 0.5922 (mmt) cc_final: 0.4897 (mmm) REVERT: C 245 TYR cc_start: 0.8457 (m-80) cc_final: 0.7785 (m-10) REVERT: C 359 ARG cc_start: 0.9456 (mtt180) cc_final: 0.9053 (mmm-85) REVERT: C 397 ARG cc_start: 0.8862 (mmt90) cc_final: 0.8503 (tpp80) REVERT: C 472 PHE cc_start: 0.8624 (m-80) cc_final: 0.8082 (m-80) REVERT: C 539 THR cc_start: 0.9101 (m) cc_final: 0.8601 (p) REVERT: C 576 MET cc_start: 0.8723 (ptt) cc_final: 0.8274 (ptt) REVERT: C 607 MET cc_start: 0.8696 (tmm) cc_final: 0.8453 (tmm) REVERT: C 636 TRP cc_start: 0.8232 (m100) cc_final: 0.7837 (m100) REVERT: C 641 MET cc_start: 0.9381 (tmm) cc_final: 0.8979 (ttm) REVERT: C 685 LYS cc_start: 0.8740 (pttm) cc_final: 0.8507 (mtmm) REVERT: C 689 VAL cc_start: 0.9182 (t) cc_final: 0.8916 (p) REVERT: C 690 ASP cc_start: 0.9123 (m-30) cc_final: 0.8842 (m-30) REVERT: C 708 LYS cc_start: 0.9619 (mttt) cc_final: 0.9307 (ptpp) REVERT: C 736 LEU cc_start: 0.9019 (mt) cc_final: 0.8740 (mt) REVERT: C 786 GLU cc_start: 0.9436 (tp30) cc_final: 0.9119 (tp30) REVERT: C 789 ASP cc_start: 0.9443 (t70) cc_final: 0.9162 (t0) REVERT: C 790 LYS cc_start: 0.9174 (mmpt) cc_final: 0.8748 (mmmt) outliers start: 1 outliers final: 0 residues processed: 683 average time/residue: 0.1501 time to fit residues: 161.6178 Evaluate side-chains 568 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 19 optimal weight: 5.9990 chunk 155 optimal weight: 0.0060 chunk 280 optimal weight: 4.9990 chunk 47 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 97 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN A 727 HIS ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 HIS C 727 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.112533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086632 restraints weight = 127010.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.090597 restraints weight = 75299.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.093543 restraints weight = 51261.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095725 restraints weight = 37892.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097391 restraints weight = 29583.659| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24452 Z= 0.141 Angle : 0.700 10.422 33152 Z= 0.370 Chirality : 0.048 0.231 3790 Planarity : 0.004 0.054 4182 Dihedral : 6.118 32.605 3280 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.13 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3028 helix: -0.27 (0.14), residues: 1232 sheet: -1.09 (0.27), residues: 334 loop : -1.79 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 489 TYR 0.037 0.002 TYR C 232 PHE 0.035 0.002 PHE C 639 TRP 0.074 0.003 TRP A 151 HIS 0.024 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00305 (24442) covalent geometry : angle 0.69630 (33132) SS BOND : bond 0.00547 ( 10) SS BOND : angle 2.89568 ( 20) hydrogen bonds : bond 0.04025 ( 1019) hydrogen bonds : angle 5.93258 ( 2959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 678 time to evaluate : 0.941 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: 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: D 80 LYS cc_start: 0.9246 (mttt) cc_final: 0.8901 (mtmt) REVERT: D 133 MET cc_start: 0.8275 (mmm) cc_final: 0.7141 (mpp) REVERT: D 160 LYS cc_start: 0.7817 (mttt) cc_final: 0.7141 (tptm) REVERT: D 264 ASN cc_start: 0.9137 (p0) cc_final: 0.8792 (p0) REVERT: D 355 TYR cc_start: 0.8455 (m-80) cc_final: 0.8125 (m-80) REVERT: D 437 ARG cc_start: 0.4959 (mtt180) cc_final: 0.4442 (mtt180) REVERT: D 448 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8496 (mp0) REVERT: D 459 PHE cc_start: 0.7779 (m-80) cc_final: 0.6594 (m-80) REVERT: D 496 MET cc_start: 0.8518 (mmt) cc_final: 0.8192 (mtt) REVERT: D 499 GLU cc_start: 0.8649 (tp30) cc_final: 0.8417 (tp30) REVERT: D 606 TRP cc_start: 0.7431 (m100) cc_final: 0.6895 (m100) REVERT: D 754 TYR cc_start: 0.8541 (m-10) cc_final: 0.8250 (m-10) REVERT: D 774 GLN cc_start: 0.9196 (mp10) cc_final: 0.8772 (mp10) REVERT: D 788 MET cc_start: 0.9350 (mtm) cc_final: 0.8930 (mtm) REVERT: D 790 GLU cc_start: 0.9557 (mp0) cc_final: 0.9311 (mp0) REVERT: A 39 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9021 (mp0) REVERT: A 125 MET cc_start: 0.8672 (mmp) cc_final: 0.8471 (mmp) REVERT: A 140 THR cc_start: 0.9386 (p) cc_final: 0.9065 (t) REVERT: A 183 LEU cc_start: 0.8580 (mt) cc_final: 0.8371 (tp) REVERT: A 225 GLU cc_start: 0.7820 (tt0) cc_final: 0.7301 (tp30) REVERT: A 248 LEU cc_start: 0.9191 (tp) cc_final: 0.8879 (tp) REVERT: A 252 ARG cc_start: 0.8424 (ptp90) cc_final: 0.8075 (ptp90) REVERT: A 357 GLN cc_start: 0.8399 (mt0) cc_final: 0.7887 (pp30) REVERT: A 358 ASN cc_start: 0.9026 (m-40) cc_final: 0.8267 (m-40) REVERT: A 477 HIS cc_start: 0.8660 (t-90) cc_final: 0.8423 (t70) REVERT: A 489 ARG cc_start: 0.5593 (mmt90) cc_final: 0.4854 (mmt90) REVERT: A 533 PHE cc_start: 0.7586 (m-80) cc_final: 0.6516 (m-80) REVERT: A 534 LYS cc_start: 0.8630 (mppt) cc_final: 0.8179 (ptmt) REVERT: A 563 TRP cc_start: 0.7873 (m100) cc_final: 0.7591 (m100) REVERT: A 611 TRP cc_start: 0.7769 (m100) cc_final: 0.7390 (m100) REVERT: A 663 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8181 (pmt-80) REVERT: A 698 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9171 (tm-30) REVERT: A 736 LEU cc_start: 0.8032 (tp) cc_final: 0.7540 (tp) REVERT: A 737 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8415 (mm-30) REVERT: A 762 MET cc_start: 0.7587 (mmm) cc_final: 0.6739 (mtp) REVERT: A 785 MET cc_start: 0.8456 (mpp) cc_final: 0.8007 (mpp) REVERT: A 801 ARG cc_start: 0.6611 (mtt180) cc_final: 0.5266 (tpt170) REVERT: B 102 ASP cc_start: 0.9382 (m-30) cc_final: 0.8842 (t70) REVERT: B 134 ILE cc_start: 0.7700 (mt) cc_final: 0.7425 (mm) REVERT: B 135 MET cc_start: 0.7507 (mmp) cc_final: 0.7230 (mmp) REVERT: B 158 MET cc_start: 0.9400 (mtt) cc_final: 0.8843 (mtt) REVERT: B 159 LEU cc_start: 0.9665 (mt) cc_final: 0.9459 (mt) REVERT: B 167 TRP cc_start: 0.7544 (m100) cc_final: 0.7286 (m100) REVERT: B 227 ILE cc_start: 0.8947 (mt) cc_final: 0.8707 (mt) REVERT: B 251 TYR cc_start: 0.5050 (m-80) cc_final: 0.3962 (m-80) REVERT: B 255 TRP cc_start: 0.8757 (m100) cc_final: 0.8289 (m-10) REVERT: B 264 ASN cc_start: 0.9169 (m-40) cc_final: 0.8893 (t0) REVERT: B 267 LEU cc_start: 0.8819 (mt) cc_final: 0.7862 (mt) REVERT: B 293 ARG cc_start: 0.9489 (mtt180) cc_final: 0.9281 (mmm-85) REVERT: B 334 LEU cc_start: 0.9597 (mt) cc_final: 0.9147 (mm) REVERT: B 355 TYR cc_start: 0.9060 (m-80) cc_final: 0.8223 (m-80) REVERT: B 385 LEU cc_start: 0.9040 (mt) cc_final: 0.8814 (mt) REVERT: B 409 VAL cc_start: 0.7443 (t) cc_final: 0.7007 (t) REVERT: B 455 CYS cc_start: 0.6707 (m) cc_final: 0.6467 (m) REVERT: B 459 PHE cc_start: 0.8778 (m-80) cc_final: 0.8116 (m-80) REVERT: B 473 PHE cc_start: 0.8127 (m-80) cc_final: 0.7599 (m-80) REVERT: B 496 MET cc_start: 0.8164 (mmm) cc_final: 0.7130 (mmm) REVERT: B 507 MET cc_start: 0.8920 (tpp) cc_final: 0.8608 (tpp) REVERT: B 653 MET cc_start: 0.8339 (mtm) cc_final: 0.7711 (tpt) REVERT: B 672 ARG cc_start: 0.9287 (mtt180) cc_final: 0.8964 (mmm160) REVERT: B 696 ASN cc_start: 0.8818 (m-40) cc_final: 0.8450 (m110) REVERT: B 700 TYR cc_start: 0.9207 (m-80) cc_final: 0.8834 (p90) REVERT: B 705 MET cc_start: 0.9060 (tpp) cc_final: 0.8773 (mmm) REVERT: B 781 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8181 (tp-100) REVERT: B 787 GLU cc_start: 0.9433 (mt-10) cc_final: 0.8844 (mp0) REVERT: B 790 GLU cc_start: 0.9343 (tp30) cc_final: 0.8775 (tp30) REVERT: B 792 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8756 (mt-10) REVERT: B 794 LEU cc_start: 0.8300 (mt) cc_final: 0.7469 (mt) REVERT: B 839 HIS cc_start: 0.8484 (p-80) cc_final: 0.8174 (p-80) REVERT: C 114 TYR cc_start: 0.9071 (m-80) cc_final: 0.8520 (m-80) REVERT: C 147 GLN cc_start: 0.9200 (mt0) cc_final: 0.8393 (mp10) REVERT: C 166 LEU cc_start: 0.9252 (mm) cc_final: 0.9051 (mm) REVERT: C 171 HIS cc_start: 0.8225 (t-90) cc_final: 0.7951 (t70) REVERT: C 303 ASP cc_start: 0.8626 (m-30) cc_final: 0.8231 (t70) REVERT: C 359 ARG cc_start: 0.9463 (mtt180) cc_final: 0.9140 (mmm-85) REVERT: C 397 ARG cc_start: 0.8840 (mmt90) cc_final: 0.8504 (tpp80) REVERT: C 513 ILE cc_start: 0.8051 (mt) cc_final: 0.7847 (mt) REVERT: C 514 VAL cc_start: 0.9189 (t) cc_final: 0.8964 (p) REVERT: C 520 ASN cc_start: 0.8204 (m110) cc_final: 0.7947 (m-40) REVERT: C 539 THR cc_start: 0.9166 (m) cc_final: 0.8705 (p) REVERT: C 576 MET cc_start: 0.8746 (ptt) cc_final: 0.8317 (ptt) REVERT: C 607 MET cc_start: 0.8797 (tmm) cc_final: 0.8564 (tmm) REVERT: C 634 MET cc_start: 0.8401 (ptt) cc_final: 0.7850 (ptp) REVERT: C 635 VAL cc_start: 0.8983 (t) cc_final: 0.8778 (t) REVERT: C 636 TRP cc_start: 0.8133 (m100) cc_final: 0.7701 (m100) REVERT: C 641 MET cc_start: 0.9423 (tmm) cc_final: 0.9046 (ttm) REVERT: C 690 ASP cc_start: 0.9093 (m-30) cc_final: 0.8852 (m-30) REVERT: C 696 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8521 (tm-30) REVERT: C 697 VAL cc_start: 0.7965 (t) cc_final: 0.7694 (t) REVERT: C 736 LEU cc_start: 0.9028 (mt) cc_final: 0.8786 (mt) REVERT: C 786 GLU cc_start: 0.9415 (tp30) cc_final: 0.9100 (tp30) REVERT: C 789 ASP cc_start: 0.9401 (t70) cc_final: 0.9058 (t0) REVERT: C 790 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8608 (mmmt) outliers start: 0 outliers final: 0 residues processed: 678 average time/residue: 0.1535 time to fit residues: 164.5255 Evaluate side-chains 562 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 24 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 249 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 HIS D 153 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.083052 restraints weight = 163765.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087244 restraints weight = 91123.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.090280 restraints weight = 60255.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092545 restraints weight = 43716.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.094218 restraints weight = 33774.224| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24452 Z= 0.189 Angle : 0.751 12.953 33152 Z= 0.397 Chirality : 0.049 0.214 3790 Planarity : 0.005 0.090 4182 Dihedral : 6.215 31.866 3280 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.09 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3028 helix: -0.28 (0.14), residues: 1232 sheet: -0.93 (0.29), residues: 310 loop : -1.82 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 518 TYR 0.035 0.002 TYR C 232 PHE 0.031 0.003 PHE D 641 TRP 0.076 0.003 TRP A 151 HIS 0.016 0.002 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00404 (24442) covalent geometry : angle 0.74769 (33132) SS BOND : bond 0.00966 ( 10) SS BOND : angle 2.95148 ( 20) hydrogen bonds : bond 0.04205 ( 1019) hydrogen bonds : angle 6.09152 ( 2959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 0.898 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: 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: D 38 VAL cc_start: 0.8693 (t) cc_final: 0.8426 (t) REVERT: D 145 PHE cc_start: 0.8279 (m-80) cc_final: 0.7837 (m-80) REVERT: D 160 LYS cc_start: 0.8029 (mttt) cc_final: 0.7436 (tttt) REVERT: D 264 ASN cc_start: 0.9375 (p0) cc_final: 0.8999 (p0) REVERT: D 272 PHE cc_start: 0.8908 (m-80) cc_final: 0.8539 (m-80) REVERT: D 355 TYR cc_start: 0.8741 (m-80) cc_final: 0.8538 (m-80) REVERT: D 437 ARG cc_start: 0.5405 (mtt180) cc_final: 0.4677 (mtt180) REVERT: D 448 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8453 (mp0) REVERT: D 459 PHE cc_start: 0.7895 (m-80) cc_final: 0.6714 (m-80) REVERT: D 473 PHE cc_start: 0.8254 (m-80) cc_final: 0.7612 (m-80) REVERT: D 499 GLU cc_start: 0.8776 (tp30) cc_final: 0.8481 (tp30) REVERT: D 507 MET cc_start: 0.8175 (tpt) cc_final: 0.7875 (tpp) REVERT: D 512 LEU cc_start: 0.8067 (mt) cc_final: 0.7789 (mt) REVERT: D 518 ARG cc_start: 0.8643 (mtt90) cc_final: 0.8405 (ptp-170) REVERT: D 524 PHE cc_start: 0.7734 (m-80) cc_final: 0.6800 (m-10) REVERT: D 534 SER cc_start: 0.8990 (p) cc_final: 0.8313 (p) REVERT: D 606 TRP cc_start: 0.7649 (m100) cc_final: 0.7196 (m100) REVERT: D 754 TYR cc_start: 0.8755 (m-10) cc_final: 0.8527 (m-10) REVERT: D 788 MET cc_start: 0.9405 (mtm) cc_final: 0.8965 (mtm) REVERT: D 790 GLU cc_start: 0.9569 (mp0) cc_final: 0.9333 (mp0) REVERT: A 39 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9097 (mp0) REVERT: A 66 THR cc_start: 0.8237 (p) cc_final: 0.8027 (p) REVERT: A 140 THR cc_start: 0.9451 (p) cc_final: 0.9161 (t) REVERT: A 146 HIS cc_start: 0.9021 (m-70) cc_final: 0.8487 (m-70) REVERT: A 209 MET cc_start: 0.9551 (tpp) cc_final: 0.9343 (tpp) REVERT: A 225 GLU cc_start: 0.7846 (tt0) cc_final: 0.7239 (tp30) REVERT: A 232 TYR cc_start: 0.8814 (m-10) cc_final: 0.8423 (m-10) REVERT: A 245 TYR cc_start: 0.8411 (m-80) cc_final: 0.8064 (m-10) REVERT: A 248 LEU cc_start: 0.9189 (tp) cc_final: 0.8874 (tp) REVERT: A 252 ARG cc_start: 0.8635 (ptp90) cc_final: 0.8188 (ptp90) REVERT: A 357 GLN cc_start: 0.8507 (mt0) cc_final: 0.8082 (pp30) REVERT: A 472 PHE cc_start: 0.8644 (m-80) cc_final: 0.7754 (m-80) REVERT: A 477 HIS cc_start: 0.8769 (t-90) cc_final: 0.8550 (t70) REVERT: A 489 ARG cc_start: 0.5597 (mmt90) cc_final: 0.4370 (tpp-160) REVERT: A 533 PHE cc_start: 0.7869 (m-80) cc_final: 0.6754 (m-80) REVERT: A 534 LYS cc_start: 0.8701 (mppt) cc_final: 0.8072 (mtpp) REVERT: A 563 TRP cc_start: 0.7921 (m100) cc_final: 0.7666 (m100) REVERT: A 611 TRP cc_start: 0.7985 (m100) cc_final: 0.7561 (m100) REVERT: A 663 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8394 (ptt-90) REVERT: A 737 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8468 (mm-30) REVERT: A 801 ARG cc_start: 0.6612 (mtt180) cc_final: 0.5234 (tpt170) REVERT: B 85 HIS cc_start: 0.9037 (m90) cc_final: 0.8756 (m90) REVERT: B 102 ASP cc_start: 0.9330 (m-30) cc_final: 0.8709 (t70) REVERT: B 134 ILE cc_start: 0.7952 (mt) cc_final: 0.7435 (mm) REVERT: B 135 MET cc_start: 0.7778 (mmp) cc_final: 0.7439 (mmp) REVERT: B 158 MET cc_start: 0.9439 (mtt) cc_final: 0.8970 (mtp) REVERT: B 159 LEU cc_start: 0.9689 (mt) cc_final: 0.9484 (mt) REVERT: B 167 TRP cc_start: 0.7936 (m100) cc_final: 0.7588 (m100) REVERT: B 227 ILE cc_start: 0.9123 (mt) cc_final: 0.8867 (mm) REVERT: B 235 GLU cc_start: 0.8539 (tt0) cc_final: 0.8257 (tt0) REVERT: B 257 VAL cc_start: 0.9152 (t) cc_final: 0.8943 (t) REVERT: B 264 ASN cc_start: 0.9250 (m-40) cc_final: 0.8963 (t0) REVERT: B 267 LEU cc_start: 0.8895 (mt) cc_final: 0.7949 (mp) REVERT: B 272 PHE cc_start: 0.8837 (m-80) cc_final: 0.8281 (m-80) REVERT: B 293 ARG cc_start: 0.9516 (mtt180) cc_final: 0.9216 (mmm-85) REVERT: B 338 MET cc_start: 0.8447 (mmp) cc_final: 0.8056 (mmm) REVERT: B 385 LEU cc_start: 0.9132 (mt) cc_final: 0.8899 (mt) REVERT: B 437 ARG cc_start: 0.5532 (mtt180) cc_final: 0.3435 (ptp-170) REVERT: B 473 PHE cc_start: 0.8385 (m-80) cc_final: 0.7944 (m-80) REVERT: B 478 TYR cc_start: 0.8305 (m-10) cc_final: 0.7659 (m-80) REVERT: B 496 MET cc_start: 0.8494 (mmm) cc_final: 0.7501 (mmm) REVERT: B 653 MET cc_start: 0.8253 (mtm) cc_final: 0.7800 (tpt) REVERT: B 696 ASN cc_start: 0.8823 (m-40) cc_final: 0.8470 (m110) REVERT: B 700 TYR cc_start: 0.9236 (m-80) cc_final: 0.8868 (p90) REVERT: B 705 MET cc_start: 0.9133 (tpp) cc_final: 0.8808 (mmm) REVERT: B 737 TYR cc_start: 0.8352 (m-10) cc_final: 0.7658 (m-80) REVERT: B 781 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8274 (tp-100) REVERT: B 787 GLU cc_start: 0.9440 (mt-10) cc_final: 0.8995 (mp0) REVERT: B 790 GLU cc_start: 0.9345 (tp30) cc_final: 0.8856 (tp30) REVERT: B 792 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8735 (mt-10) REVERT: B 794 LEU cc_start: 0.8356 (mt) cc_final: 0.7550 (mt) REVERT: B 839 HIS cc_start: 0.8543 (p-80) cc_final: 0.8201 (p-80) REVERT: C 114 TYR cc_start: 0.9230 (m-80) cc_final: 0.8577 (m-80) REVERT: C 166 LEU cc_start: 0.9239 (mm) cc_final: 0.9022 (mm) REVERT: C 171 HIS cc_start: 0.8402 (t-90) cc_final: 0.7981 (t70) REVERT: C 245 TYR cc_start: 0.8724 (m-80) cc_final: 0.7955 (m-10) REVERT: C 261 TYR cc_start: 0.8797 (m-10) cc_final: 0.8415 (m-10) REVERT: C 303 ASP cc_start: 0.8946 (m-30) cc_final: 0.8424 (t0) REVERT: C 359 ARG cc_start: 0.9414 (mtt180) cc_final: 0.9111 (mmm-85) REVERT: C 434 VAL cc_start: 0.8800 (t) cc_final: 0.8249 (m) REVERT: C 456 TYR cc_start: 0.6005 (m-80) cc_final: 0.5122 (m-80) REVERT: C 472 PHE cc_start: 0.8576 (m-80) cc_final: 0.8045 (m-80) REVERT: C 477 HIS cc_start: 0.9078 (m90) cc_final: 0.8813 (m90) REVERT: C 513 ILE cc_start: 0.8218 (mt) cc_final: 0.7967 (mt) REVERT: C 520 ASN cc_start: 0.8486 (m110) cc_final: 0.8074 (m110) REVERT: C 539 THR cc_start: 0.9258 (m) cc_final: 0.8833 (p) REVERT: C 576 MET cc_start: 0.8904 (ptt) cc_final: 0.8467 (ptt) REVERT: C 607 MET cc_start: 0.8882 (tmm) cc_final: 0.8646 (tmm) REVERT: C 634 MET cc_start: 0.8518 (ptt) cc_final: 0.8160 (ptt) REVERT: C 635 VAL cc_start: 0.8990 (t) cc_final: 0.8617 (t) REVERT: C 636 TRP cc_start: 0.8199 (m100) cc_final: 0.7813 (m100) REVERT: C 641 MET cc_start: 0.9432 (tmm) cc_final: 0.9109 (ttm) REVERT: C 696 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8613 (tm-30) REVERT: C 716 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8134 (mm-30) REVERT: C 736 LEU cc_start: 0.8969 (mt) cc_final: 0.8624 (mt) outliers start: 0 outliers final: 0 residues processed: 656 average time/residue: 0.1505 time to fit residues: 156.9345 Evaluate side-chains 546 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 546 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 242 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 197 optimal weight: 20.0000 chunk 180 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 432 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 162 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.110360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.084637 restraints weight = 141259.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088539 restraints weight = 83390.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.091393 restraints weight = 56739.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.093517 restraints weight = 41945.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.095062 restraints weight = 32870.215| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 24452 Z= 0.155 Angle : 0.725 15.067 33152 Z= 0.383 Chirality : 0.049 0.256 3790 Planarity : 0.005 0.125 4182 Dihedral : 6.101 31.352 3280 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.33 % Favored : 91.40 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.57 (0.15), residues: 3028 helix: -0.18 (0.14), residues: 1244 sheet: -0.99 (0.28), residues: 316 loop : -1.81 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 390 TYR 0.048 0.002 TYR C 392 PHE 0.027 0.002 PHE A 639 TRP 0.084 0.003 TRP A 151 HIS 0.026 0.002 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00335 (24442) covalent geometry : angle 0.72092 (33132) SS BOND : bond 0.01180 ( 10) SS BOND : angle 3.20509 ( 20) hydrogen bonds : bond 0.04075 ( 1019) hydrogen bonds : angle 5.94785 ( 2959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 0.891 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: 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: D 80 LYS cc_start: 0.9199 (mttt) cc_final: 0.8980 (mttt) REVERT: D 133 MET cc_start: 0.8518 (mmm) cc_final: 0.7784 (mpp) REVERT: D 160 LYS cc_start: 0.8102 (mttt) cc_final: 0.7506 (tttt) REVERT: D 264 ASN cc_start: 0.9444 (p0) cc_final: 0.9106 (p0) REVERT: D 272 PHE cc_start: 0.8870 (m-80) cc_final: 0.8501 (m-80) REVERT: D 437 ARG cc_start: 0.5360 (mtt180) cc_final: 0.4904 (mtt180) REVERT: D 448 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8460 (mp0) REVERT: D 459 PHE cc_start: 0.7901 (m-80) cc_final: 0.6713 (m-80) REVERT: D 473 PHE cc_start: 0.8250 (m-80) cc_final: 0.7697 (m-80) REVERT: D 499 GLU cc_start: 0.8789 (tp30) cc_final: 0.8461 (tp30) REVERT: D 507 MET cc_start: 0.8219 (tpt) cc_final: 0.7846 (tpp) REVERT: D 512 LEU cc_start: 0.7828 (mt) cc_final: 0.7593 (mt) REVERT: D 518 ARG cc_start: 0.8747 (mtt90) cc_final: 0.8372 (ptp-170) REVERT: D 524 PHE cc_start: 0.7632 (m-80) cc_final: 0.6701 (m-10) REVERT: D 562 MET cc_start: 0.8555 (mpp) cc_final: 0.8192 (mpp) REVERT: D 606 TRP cc_start: 0.7540 (m100) cc_final: 0.7012 (m100) REVERT: D 692 ARG cc_start: 0.8129 (tpp-160) cc_final: 0.7738 (tpm170) REVERT: D 788 MET cc_start: 0.9346 (mtm) cc_final: 0.9010 (mtm) REVERT: D 790 GLU cc_start: 0.9561 (mp0) cc_final: 0.9294 (mp0) REVERT: A 39 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9095 (mp0) REVERT: A 66 THR cc_start: 0.8267 (p) cc_final: 0.8043 (p) REVERT: A 140 THR cc_start: 0.9484 (p) cc_final: 0.9170 (t) REVERT: A 146 HIS cc_start: 0.8986 (m-70) cc_final: 0.8464 (m-70) REVERT: A 183 LEU cc_start: 0.8723 (mm) cc_final: 0.8441 (tp) REVERT: A 225 GLU cc_start: 0.7832 (tt0) cc_final: 0.7226 (tp30) REVERT: A 232 TYR cc_start: 0.8842 (m-10) cc_final: 0.8455 (m-10) REVERT: A 245 TYR cc_start: 0.8295 (m-80) cc_final: 0.7578 (m-80) REVERT: A 248 LEU cc_start: 0.9138 (tp) cc_final: 0.8599 (tp) REVERT: A 252 ARG cc_start: 0.8620 (ptp90) cc_final: 0.8240 (ptp90) REVERT: A 357 GLN cc_start: 0.8562 (mt0) cc_final: 0.8140 (pp30) REVERT: A 400 ILE cc_start: 0.8991 (mp) cc_final: 0.8328 (mp) REVERT: A 489 ARG cc_start: 0.5490 (mmt90) cc_final: 0.4993 (tpp-160) REVERT: A 502 MET cc_start: 0.8684 (mtm) cc_final: 0.8452 (mtm) REVERT: A 611 TRP cc_start: 0.7977 (m100) cc_final: 0.7543 (m100) REVERT: A 663 ARG cc_start: 0.8633 (mtt180) cc_final: 0.8272 (pmt-80) REVERT: A 737 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8490 (mm-30) REVERT: A 789 ASP cc_start: 0.9099 (t70) cc_final: 0.8891 (t0) REVERT: A 801 ARG cc_start: 0.6620 (mtt180) cc_final: 0.5246 (tpt170) REVERT: B 102 ASP cc_start: 0.9364 (m-30) cc_final: 0.8697 (t70) REVERT: B 134 ILE cc_start: 0.7870 (mt) cc_final: 0.7404 (mm) REVERT: B 135 MET cc_start: 0.7824 (mmp) cc_final: 0.7486 (mmp) REVERT: B 158 MET cc_start: 0.9459 (mtt) cc_final: 0.8990 (mtp) REVERT: B 167 TRP cc_start: 0.7869 (m100) cc_final: 0.7616 (m100) REVERT: B 235 GLU cc_start: 0.8516 (tt0) cc_final: 0.8098 (tt0) REVERT: B 257 VAL cc_start: 0.9277 (t) cc_final: 0.9045 (t) REVERT: B 264 ASN cc_start: 0.9231 (m-40) cc_final: 0.8970 (t0) REVERT: B 267 LEU cc_start: 0.8901 (mt) cc_final: 0.7978 (mp) REVERT: B 293 ARG cc_start: 0.9469 (mtt180) cc_final: 0.9156 (mmm-85) REVERT: B 338 MET cc_start: 0.8637 (mmp) cc_final: 0.8221 (mmm) REVERT: B 405 HIS cc_start: 0.7948 (m-70) cc_final: 0.7732 (m170) REVERT: B 437 ARG cc_start: 0.5486 (mtt180) cc_final: 0.3167 (ptp-110) REVERT: B 473 PHE cc_start: 0.8381 (m-80) cc_final: 0.7922 (m-80) REVERT: B 496 MET cc_start: 0.8485 (mmm) cc_final: 0.7630 (mmm) REVERT: B 536 MET cc_start: 0.8549 (tmm) cc_final: 0.7965 (tmm) REVERT: B 653 MET cc_start: 0.8245 (mtm) cc_final: 0.7782 (tpt) REVERT: B 696 ASN cc_start: 0.8807 (m-40) cc_final: 0.8465 (m110) REVERT: B 700 TYR cc_start: 0.9244 (m-80) cc_final: 0.8871 (p90) REVERT: B 705 MET cc_start: 0.9129 (tpp) cc_final: 0.8820 (mmm) REVERT: B 737 TYR cc_start: 0.8339 (m-10) cc_final: 0.7672 (m-80) REVERT: B 781 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8186 (tp-100) REVERT: B 785 ASP cc_start: 0.6787 (m-30) cc_final: 0.6075 (m-30) REVERT: B 787 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9000 (mp0) REVERT: B 790 GLU cc_start: 0.9335 (tp30) cc_final: 0.8877 (tp30) REVERT: B 792 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8836 (mt-10) REVERT: B 794 LEU cc_start: 0.8452 (mt) cc_final: 0.7648 (mt) REVERT: B 839 HIS cc_start: 0.8587 (p-80) cc_final: 0.8232 (p-80) REVERT: C 114 TYR cc_start: 0.9235 (m-80) cc_final: 0.8584 (m-80) REVERT: C 147 GLN cc_start: 0.9336 (mt0) cc_final: 0.8508 (mp10) REVERT: C 166 LEU cc_start: 0.9216 (mm) cc_final: 0.8926 (mm) REVERT: C 171 HIS cc_start: 0.8390 (t-90) cc_final: 0.7943 (t70) REVERT: C 172 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8074 (mm-30) REVERT: C 209 MET cc_start: 0.9017 (tpt) cc_final: 0.8816 (tpp) REVERT: C 303 ASP cc_start: 0.8959 (m-30) cc_final: 0.8424 (t0) REVERT: C 359 ARG cc_start: 0.9412 (mtt180) cc_final: 0.9027 (mmm-85) REVERT: C 539 THR cc_start: 0.9295 (m) cc_final: 0.8860 (p) REVERT: C 634 MET cc_start: 0.8513 (ptt) cc_final: 0.8213 (ptt) REVERT: C 635 VAL cc_start: 0.8971 (t) cc_final: 0.8609 (t) REVERT: C 636 TRP cc_start: 0.8231 (m100) cc_final: 0.7931 (m100) REVERT: C 641 MET cc_start: 0.9424 (tmm) cc_final: 0.8961 (ttt) REVERT: C 690 ASP cc_start: 0.9185 (m-30) cc_final: 0.8967 (m-30) REVERT: C 716 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7987 (mm-30) REVERT: C 736 LEU cc_start: 0.8910 (mt) cc_final: 0.8595 (mt) REVERT: C 786 GLU cc_start: 0.9504 (tp30) cc_final: 0.9029 (tp30) REVERT: C 789 ASP cc_start: 0.9510 (t0) cc_final: 0.9309 (t0) REVERT: C 790 LYS cc_start: 0.9258 (mmpt) cc_final: 0.8806 (mmmt) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.1499 time to fit residues: 155.0326 Evaluate side-chains 558 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 131 optimal weight: 9.9990 chunk 261 optimal weight: 0.0980 chunk 98 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 300 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 432 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 GLN ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN C 559 GLN C 650 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.116125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.088536 restraints weight = 161537.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.092892 restraints weight = 88790.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.096021 restraints weight = 58306.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.098419 restraints weight = 42294.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.100196 restraints weight = 32616.283| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24452 Z= 0.134 Angle : 0.716 11.942 33152 Z= 0.374 Chirality : 0.049 0.294 3790 Planarity : 0.004 0.068 4182 Dihedral : 5.920 30.736 3280 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.40 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.46 (0.15), residues: 3028 helix: -0.08 (0.14), residues: 1240 sheet: -1.07 (0.28), residues: 320 loop : -1.72 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 437 TYR 0.026 0.002 TYR C 392 PHE 0.025 0.002 PHE B 641 TRP 0.087 0.003 TRP A 151 HIS 0.016 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00296 (24442) covalent geometry : angle 0.71244 (33132) SS BOND : bond 0.00507 ( 10) SS BOND : angle 3.04185 ( 20) hydrogen bonds : bond 0.03954 ( 1019) hydrogen bonds : angle 5.81971 ( 2959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 0.577 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: 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: D 80 LYS cc_start: 0.9212 (mttt) cc_final: 0.8985 (mttt) REVERT: D 133 MET cc_start: 0.8545 (mmm) cc_final: 0.7771 (mpp) REVERT: D 160 LYS cc_start: 0.8109 (mttt) cc_final: 0.7569 (tttt) REVERT: D 264 ASN cc_start: 0.9424 (p0) cc_final: 0.9087 (p0) REVERT: D 272 PHE cc_start: 0.8775 (m-80) cc_final: 0.8474 (m-80) REVERT: D 437 ARG cc_start: 0.5258 (mtt180) cc_final: 0.4816 (mtt180) REVERT: D 448 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8596 (mp0) REVERT: D 459 PHE cc_start: 0.7930 (m-80) cc_final: 0.6751 (m-80) REVERT: D 473 PHE cc_start: 0.8220 (m-80) cc_final: 0.7653 (m-80) REVERT: D 499 GLU cc_start: 0.8779 (tp30) cc_final: 0.8447 (tp30) REVERT: D 507 MET cc_start: 0.8342 (tpt) cc_final: 0.7984 (tpp) REVERT: D 512 LEU cc_start: 0.7674 (mt) cc_final: 0.7396 (mt) REVERT: D 534 SER cc_start: 0.9099 (p) cc_final: 0.8421 (p) REVERT: D 606 TRP cc_start: 0.7412 (m100) cc_final: 0.6905 (m100) REVERT: D 788 MET cc_start: 0.9342 (mtm) cc_final: 0.8841 (mtm) REVERT: A 39 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9048 (mp0) REVERT: A 66 THR cc_start: 0.8225 (p) cc_final: 0.8008 (p) REVERT: A 125 MET cc_start: 0.9056 (mmp) cc_final: 0.8672 (mmp) REVERT: A 140 THR cc_start: 0.9487 (p) cc_final: 0.9188 (t) REVERT: A 146 HIS cc_start: 0.8932 (m-70) cc_final: 0.8444 (m-70) REVERT: A 183 LEU cc_start: 0.8734 (mm) cc_final: 0.8468 (tp) REVERT: A 225 GLU cc_start: 0.7732 (tt0) cc_final: 0.7154 (tp30) REVERT: A 232 TYR cc_start: 0.8860 (m-10) cc_final: 0.8446 (m-10) REVERT: A 245 TYR cc_start: 0.8434 (m-80) cc_final: 0.8013 (m-10) REVERT: A 248 LEU cc_start: 0.9129 (tp) cc_final: 0.8922 (tp) REVERT: A 252 ARG cc_start: 0.8545 (ptp90) cc_final: 0.8071 (ptp90) REVERT: A 357 GLN cc_start: 0.8528 (mt0) cc_final: 0.8131 (pp30) REVERT: A 397 ARG cc_start: 0.9592 (mtt180) cc_final: 0.9124 (mmp80) REVERT: A 472 PHE cc_start: 0.8307 (m-80) cc_final: 0.7951 (m-10) REVERT: A 477 HIS cc_start: 0.8831 (t70) cc_final: 0.8580 (t70) REVERT: A 489 ARG cc_start: 0.5470 (mmt90) cc_final: 0.4640 (tpp-160) REVERT: A 522 GLU cc_start: 0.8707 (pt0) cc_final: 0.8323 (tp30) REVERT: A 536 GLN cc_start: 0.7919 (mp-120) cc_final: 0.7591 (mp10) REVERT: A 611 TRP cc_start: 0.7992 (m100) cc_final: 0.7583 (m100) REVERT: A 663 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8340 (pmt-80) REVERT: A 683 THR cc_start: 0.8378 (p) cc_final: 0.8149 (t) REVERT: A 737 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8537 (mm-30) REVERT: A 789 ASP cc_start: 0.9121 (t70) cc_final: 0.8904 (t0) REVERT: B 100 PHE cc_start: 0.9281 (m-80) cc_final: 0.9044 (m-80) REVERT: B 102 ASP cc_start: 0.9294 (m-30) cc_final: 0.8648 (t70) REVERT: B 134 ILE cc_start: 0.7979 (mt) cc_final: 0.7558 (mm) REVERT: B 135 MET cc_start: 0.7705 (mmp) cc_final: 0.7466 (mmp) REVERT: B 158 MET cc_start: 0.9479 (mtt) cc_final: 0.9078 (mtp) REVERT: B 200 MET cc_start: 0.8503 (tmm) cc_final: 0.7777 (tmm) REVERT: B 227 ILE cc_start: 0.9161 (mm) cc_final: 0.8830 (mm) REVERT: B 235 GLU cc_start: 0.8352 (tt0) cc_final: 0.8102 (tt0) REVERT: B 255 TRP cc_start: 0.8626 (m100) cc_final: 0.8315 (m-10) REVERT: B 257 VAL cc_start: 0.9214 (t) cc_final: 0.8984 (t) REVERT: B 267 LEU cc_start: 0.8882 (mt) cc_final: 0.7964 (mp) REVERT: B 293 ARG cc_start: 0.9513 (mtt180) cc_final: 0.9162 (mmm-85) REVERT: B 338 MET cc_start: 0.8705 (mmp) cc_final: 0.8301 (mmm) REVERT: B 385 LEU cc_start: 0.8871 (mm) cc_final: 0.8428 (mt) REVERT: B 437 ARG cc_start: 0.4998 (mtt180) cc_final: 0.3256 (ptp-170) REVERT: B 473 PHE cc_start: 0.8379 (m-80) cc_final: 0.7929 (m-80) REVERT: B 496 MET cc_start: 0.8511 (mmm) cc_final: 0.7765 (mmm) REVERT: B 507 MET cc_start: 0.8837 (tpp) cc_final: 0.8620 (tpp) REVERT: B 536 MET cc_start: 0.8730 (tmm) cc_final: 0.8128 (tmm) REVERT: B 562 MET cc_start: 0.9345 (mpp) cc_final: 0.9019 (mpp) REVERT: B 653 MET cc_start: 0.8188 (mtm) cc_final: 0.7813 (tpt) REVERT: B 696 ASN cc_start: 0.8748 (m-40) cc_final: 0.8368 (m110) REVERT: B 700 TYR cc_start: 0.9228 (m-80) cc_final: 0.8879 (p90) REVERT: B 705 MET cc_start: 0.9029 (tpp) cc_final: 0.8737 (mmm) REVERT: B 737 TYR cc_start: 0.8306 (m-10) cc_final: 0.7693 (m-80) REVERT: B 781 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8211 (tp-100) REVERT: B 785 ASP cc_start: 0.6688 (m-30) cc_final: 0.6049 (m-30) REVERT: B 787 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9017 (mp0) REVERT: B 790 GLU cc_start: 0.9327 (tp30) cc_final: 0.8817 (tp30) REVERT: B 792 GLU cc_start: 0.9354 (mt-10) cc_final: 0.8832 (mt-10) REVERT: B 794 LEU cc_start: 0.8359 (mt) cc_final: 0.7501 (mt) REVERT: B 839 HIS cc_start: 0.8577 (p-80) cc_final: 0.8223 (p-80) REVERT: C 114 TYR cc_start: 0.9228 (m-80) cc_final: 0.8628 (m-80) REVERT: C 160 TRP cc_start: 0.8369 (m100) cc_final: 0.7660 (m100) REVERT: C 166 LEU cc_start: 0.9263 (mm) cc_final: 0.8822 (mm) REVERT: C 171 HIS cc_start: 0.8290 (t-90) cc_final: 0.7832 (t70) REVERT: C 172 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8132 (mm-30) REVERT: C 197 PHE cc_start: 0.8436 (m-10) cc_final: 0.8154 (m-80) REVERT: C 303 ASP cc_start: 0.8937 (m-30) cc_final: 0.8395 (t0) REVERT: C 359 ARG cc_start: 0.9375 (mtt180) cc_final: 0.9102 (mmm-85) REVERT: C 405 GLN cc_start: 0.9518 (tp-100) cc_final: 0.8919 (tm-30) REVERT: C 539 THR cc_start: 0.9328 (m) cc_final: 0.8978 (p) REVERT: C 607 MET cc_start: 0.9029 (tmm) cc_final: 0.8686 (tmm) REVERT: C 634 MET cc_start: 0.8471 (ptt) cc_final: 0.8183 (ptt) REVERT: C 635 VAL cc_start: 0.8985 (t) cc_final: 0.8625 (t) REVERT: C 636 TRP cc_start: 0.8373 (m100) cc_final: 0.7928 (m100) REVERT: C 641 MET cc_start: 0.9417 (tmm) cc_final: 0.8961 (ttt) REVERT: C 690 ASP cc_start: 0.9185 (m-30) cc_final: 0.8961 (m-30) REVERT: C 736 LEU cc_start: 0.8943 (mt) cc_final: 0.8611 (mt) REVERT: C 786 GLU cc_start: 0.9467 (tp30) cc_final: 0.8930 (tp30) REVERT: C 789 ASP cc_start: 0.9466 (t0) cc_final: 0.9214 (t0) REVERT: C 790 LYS cc_start: 0.9165 (mmpt) cc_final: 0.8724 (mmmt) outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.1513 time to fit residues: 156.3569 Evaluate side-chains 568 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 277 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 182 optimal weight: 50.0000 chunk 143 optimal weight: 10.0000 chunk 175 optimal weight: 6.9990 chunk 18 optimal weight: 0.4980 chunk 186 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 273 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 161 ASN A 171 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 650 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.109555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.083539 restraints weight = 157149.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.087586 restraints weight = 88670.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.090547 restraints weight = 58958.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092728 restraints weight = 43025.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094386 restraints weight = 33400.176| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 24452 Z= 0.158 Angle : 0.715 12.287 33152 Z= 0.377 Chirality : 0.049 0.330 3790 Planarity : 0.004 0.049 4182 Dihedral : 5.897 30.236 3280 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.93 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.39 (0.15), residues: 3028 helix: 0.02 (0.15), residues: 1240 sheet: -1.04 (0.28), residues: 320 loop : -1.71 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 390 TYR 0.025 0.002 TYR C 232 PHE 0.032 0.002 PHE A 137 TRP 0.090 0.003 TRP A 151 HIS 0.014 0.002 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00350 (24442) covalent geometry : angle 0.71062 (33132) SS BOND : bond 0.00413 ( 10) SS BOND : angle 3.23661 ( 20) hydrogen bonds : bond 0.03989 ( 1019) hydrogen bonds : angle 5.87560 ( 2959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 0.966 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: 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: D 80 LYS cc_start: 0.9189 (mttt) cc_final: 0.8978 (mttt) REVERT: D 133 MET cc_start: 0.8583 (mmm) cc_final: 0.7697 (mpp) REVERT: D 246 LEU cc_start: 0.8773 (mt) cc_final: 0.8458 (mt) REVERT: D 264 ASN cc_start: 0.9507 (p0) cc_final: 0.9165 (p0) REVERT: D 437 ARG cc_start: 0.5525 (mtt180) cc_final: 0.5046 (mtt180) REVERT: D 448 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8595 (mp0) REVERT: D 459 PHE cc_start: 0.7841 (m-80) cc_final: 0.6746 (m-80) REVERT: D 473 PHE cc_start: 0.8297 (m-80) cc_final: 0.7781 (m-80) REVERT: D 499 GLU cc_start: 0.8947 (tp30) cc_final: 0.8522 (tp30) REVERT: D 507 MET cc_start: 0.8422 (tpt) cc_final: 0.8010 (tpp) REVERT: D 512 LEU cc_start: 0.8055 (mt) cc_final: 0.7747 (mt) REVERT: D 517 GLU cc_start: 0.9131 (tt0) cc_final: 0.8268 (tp30) REVERT: D 520 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8053 (mt-10) REVERT: D 534 SER cc_start: 0.8344 (p) cc_final: 0.7664 (p) REVERT: D 562 MET cc_start: 0.8657 (mpp) cc_final: 0.8357 (mpp) REVERT: D 606 TRP cc_start: 0.7504 (m100) cc_final: 0.7026 (m100) REVERT: D 735 LEU cc_start: 0.8966 (mt) cc_final: 0.8573 (mt) REVERT: D 788 MET cc_start: 0.9125 (mtm) cc_final: 0.8841 (mtm) REVERT: A 39 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9081 (mp0) REVERT: A 66 THR cc_start: 0.8283 (p) cc_final: 0.8051 (p) REVERT: A 125 MET cc_start: 0.9034 (mmp) cc_final: 0.8584 (mmp) REVERT: A 140 THR cc_start: 0.9483 (p) cc_final: 0.9198 (t) REVERT: A 146 HIS cc_start: 0.9132 (m-70) cc_final: 0.8614 (m-70) REVERT: A 183 LEU cc_start: 0.8729 (mm) cc_final: 0.8528 (tp) REVERT: A 225 GLU cc_start: 0.7781 (tt0) cc_final: 0.7197 (tp30) REVERT: A 232 TYR cc_start: 0.8974 (m-10) cc_final: 0.8608 (m-10) REVERT: A 245 TYR cc_start: 0.8428 (m-80) cc_final: 0.7782 (m-80) REVERT: A 248 LEU cc_start: 0.9130 (tp) cc_final: 0.8805 (tp) REVERT: A 252 ARG cc_start: 0.8657 (ptp90) cc_final: 0.8178 (ptp90) REVERT: A 357 GLN cc_start: 0.8559 (mt0) cc_final: 0.8060 (pp30) REVERT: A 358 ASN cc_start: 0.9417 (m-40) cc_final: 0.8623 (m110) REVERT: A 397 ARG cc_start: 0.9609 (mtt180) cc_final: 0.9225 (mmt180) REVERT: A 472 PHE cc_start: 0.8456 (m-80) cc_final: 0.8121 (m-10) REVERT: A 489 ARG cc_start: 0.5424 (mmt90) cc_final: 0.4641 (tpp-160) REVERT: A 529 PHE cc_start: 0.7764 (m-10) cc_final: 0.7536 (m-10) REVERT: A 533 PHE cc_start: 0.7504 (m-80) cc_final: 0.7278 (m-80) REVERT: A 611 TRP cc_start: 0.8024 (m100) cc_final: 0.7599 (m100) REVERT: A 663 ARG cc_start: 0.8740 (mtt180) cc_final: 0.8501 (ppt170) REVERT: A 736 LEU cc_start: 0.8154 (tp) cc_final: 0.7650 (tp) REVERT: A 737 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8551 (mm-30) REVERT: A 789 ASP cc_start: 0.9161 (t70) cc_final: 0.8960 (t0) REVERT: B 100 PHE cc_start: 0.9357 (m-80) cc_final: 0.9129 (m-80) REVERT: B 102 ASP cc_start: 0.9319 (m-30) cc_final: 0.8703 (t0) REVERT: B 134 ILE cc_start: 0.7862 (mt) cc_final: 0.7537 (mm) REVERT: B 135 MET cc_start: 0.7811 (mmp) cc_final: 0.7548 (mmp) REVERT: B 158 MET cc_start: 0.9508 (mtt) cc_final: 0.9164 (mtp) REVERT: B 235 GLU cc_start: 0.8479 (tt0) cc_final: 0.8208 (tt0) REVERT: B 255 TRP cc_start: 0.8809 (m100) cc_final: 0.8452 (m-10) REVERT: B 264 ASN cc_start: 0.8546 (t0) cc_final: 0.8320 (t0) REVERT: B 267 LEU cc_start: 0.8739 (mt) cc_final: 0.8212 (mp) REVERT: B 293 ARG cc_start: 0.9502 (mtt180) cc_final: 0.9152 (mmm-85) REVERT: B 338 MET cc_start: 0.8731 (mmp) cc_final: 0.8343 (mmm) REVERT: B 385 LEU cc_start: 0.8844 (mm) cc_final: 0.8381 (mt) REVERT: B 437 ARG cc_start: 0.5505 (mtt180) cc_final: 0.2997 (ptp-110) REVERT: B 473 PHE cc_start: 0.8453 (m-80) cc_final: 0.8011 (m-80) REVERT: B 496 MET cc_start: 0.8671 (mmm) cc_final: 0.7911 (mmm) REVERT: B 507 MET cc_start: 0.8946 (tpp) cc_final: 0.8498 (tpt) REVERT: B 536 MET cc_start: 0.8761 (tmm) cc_final: 0.8545 (tmm) REVERT: B 653 MET cc_start: 0.8153 (mtm) cc_final: 0.7829 (tpt) REVERT: B 696 ASN cc_start: 0.8708 (m-40) cc_final: 0.8336 (m110) REVERT: B 700 TYR cc_start: 0.9280 (m-80) cc_final: 0.8900 (p90) REVERT: B 705 MET cc_start: 0.9069 (tpp) cc_final: 0.8813 (mmm) REVERT: B 781 GLN cc_start: 0.8617 (tp-100) cc_final: 0.8088 (tp-100) REVERT: B 785 ASP cc_start: 0.6671 (m-30) cc_final: 0.5819 (m-30) REVERT: B 787 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8789 (mp0) REVERT: B 790 GLU cc_start: 0.9351 (tp30) cc_final: 0.8900 (tp30) REVERT: B 792 GLU cc_start: 0.9379 (mt-10) cc_final: 0.8871 (mt-10) REVERT: B 794 LEU cc_start: 0.8400 (mt) cc_final: 0.7581 (mt) REVERT: B 839 HIS cc_start: 0.8647 (p-80) cc_final: 0.8401 (m90) REVERT: C 114 TYR cc_start: 0.9303 (m-80) cc_final: 0.8644 (m-80) REVERT: C 127 ILE cc_start: 0.9381 (mt) cc_final: 0.9174 (tp) REVERT: C 166 LEU cc_start: 0.9318 (mm) cc_final: 0.9084 (mm) REVERT: C 171 HIS cc_start: 0.8371 (t-90) cc_final: 0.7718 (t-90) REVERT: C 172 GLU cc_start: 0.8682 (mt-10) cc_final: 0.7646 (mm-30) REVERT: C 197 PHE cc_start: 0.8494 (m-10) cc_final: 0.8193 (m-80) REVERT: C 245 TYR cc_start: 0.8700 (m-80) cc_final: 0.8453 (m-80) REVERT: C 303 ASP cc_start: 0.9084 (m-30) cc_final: 0.8486 (t0) REVERT: C 359 ARG cc_start: 0.9355 (mtt180) cc_final: 0.8915 (mmm-85) REVERT: C 477 HIS cc_start: 0.9183 (m90) cc_final: 0.8958 (m90) REVERT: C 520 ASN cc_start: 0.8350 (m110) cc_final: 0.8026 (m-40) REVERT: C 539 THR cc_start: 0.9330 (m) cc_final: 0.8989 (p) REVERT: C 634 MET cc_start: 0.8492 (ptt) cc_final: 0.8205 (ptt) REVERT: C 635 VAL cc_start: 0.8978 (t) cc_final: 0.8643 (t) REVERT: C 636 TRP cc_start: 0.8501 (m100) cc_final: 0.8033 (m100) REVERT: C 641 MET cc_start: 0.9415 (tmm) cc_final: 0.8951 (ttt) REVERT: C 696 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 736 LEU cc_start: 0.8913 (mt) cc_final: 0.8579 (mt) REVERT: C 747 VAL cc_start: 0.8727 (t) cc_final: 0.8474 (m) REVERT: C 786 GLU cc_start: 0.9529 (tp30) cc_final: 0.9008 (tp30) REVERT: C 789 ASP cc_start: 0.9472 (t0) cc_final: 0.9222 (t0) REVERT: C 790 LYS cc_start: 0.9205 (mmpt) cc_final: 0.8786 (mmmt) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.1449 time to fit residues: 150.7864 Evaluate side-chains 551 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 62 optimal weight: 0.0270 chunk 135 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 265 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 251 optimal weight: 0.0570 chunk 177 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 111 GLN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN C 650 ASN C 782 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.110500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.083237 restraints weight = 175242.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087591 restraints weight = 95049.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.090783 restraints weight = 61775.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093116 restraints weight = 44442.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.094915 restraints weight = 34149.475| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.8175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24452 Z= 0.140 Angle : 0.730 12.966 33152 Z= 0.380 Chirality : 0.049 0.369 3790 Planarity : 0.004 0.050 4182 Dihedral : 5.844 29.818 3280 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.60 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.38 (0.15), residues: 3028 helix: 0.04 (0.15), residues: 1236 sheet: -1.03 (0.29), residues: 318 loop : -1.72 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 692 TYR 0.019 0.002 TYR A 703 PHE 0.030 0.002 PHE D 641 TRP 0.087 0.003 TRP A 151 HIS 0.017 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00313 (24442) covalent geometry : angle 0.72534 (33132) SS BOND : bond 0.00348 ( 10) SS BOND : angle 3.34229 ( 20) hydrogen bonds : bond 0.03902 ( 1019) hydrogen bonds : angle 5.76806 ( 2959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4920.23 seconds wall clock time: 85 minutes 19.67 seconds (5119.67 seconds total)