Starting phenix.real_space_refine on Mon Sep 14 15:38:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.cif Found real_map, /net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.cif" model { file = "/net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5weo_8823/09_2026/5weo_8823.map" } resolution = 4.2 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 172 5.16 5 Cl 4 4.86 5 C 20049 2.51 5 N 5139 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31168 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7765 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 962} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 7753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7753 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 961} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7765 Classifications: {'peptide': 988} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 962} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7749 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 21, 'TRANS': 961} Chain breaks: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.28, per 1000 atoms: 0.20 Number of scatterers: 31168 At special positions: 0 Unit cell: (115.56, 169.56, 199.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 172 16.00 O 5804 8.00 N 5139 7.00 C 20049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7252 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 40 sheets defined 48.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.635A pdb=" N SER A 37 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 81 through 93 removed outlier: 4.078A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 139 through 142 Processing helix chain 'A' and resid 143 through 156 removed outlier: 3.625A pdb=" N LEU A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.718A pdb=" N LYS A 172 " --> pdb=" O ASN A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.923A pdb=" N ARG A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 212 removed outlier: 4.196A pdb=" N ASP A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.688A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 302 removed outlier: 3.769A pdb=" N VAL A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.619A pdb=" N ASP A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.810A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.643A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.850A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 624 removed outlier: 3.648A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 604 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.795A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.728A pdb=" N GLY A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.849A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 792 through 820 removed outlier: 4.184A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1028 removed outlier: 3.537A pdb=" N LEU A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A1014 " --> pdb=" O LEU A1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A1024 " --> pdb=" O PHE A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 Processing helix chain 'A' and resid 1104 through 1121 removed outlier: 3.799A pdb=" N LEU A1114 " --> pdb=" O SER A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1125 removed outlier: 3.769A pdb=" N GLU A1125 " --> pdb=" O ALA A1122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1122 through 1125' Processing helix chain 'A' and resid 1132 through 1161 removed outlier: 3.555A pdb=" N SER A1136 " --> pdb=" O ASN A1132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A1138 " --> pdb=" O ILE A1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A1139 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A1141 " --> pdb=" O ALA A1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A1160 " --> pdb=" O ILE A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1209 removed outlier: 4.276A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A1183 " --> pdb=" O PHE A1179 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A1190 " --> pdb=" O PHE A1186 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A1195 " --> pdb=" O MET A1191 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.635A pdb=" N SER B 37 " --> pdb=" O MET B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 69 Processing helix chain 'B' and resid 81 through 93 removed outlier: 4.078A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 143 through 156 removed outlier: 3.625A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.718A pdb=" N LYS B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.923A pdb=" N ARG B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 removed outlier: 4.197A pdb=" N ASP B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.688A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 3.769A pdb=" N VAL B 289 " --> pdb=" O THR B 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.618A pdb=" N ASP B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 430 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.811A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 519 removed outlier: 3.518A pdb=" N SER B 516 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 517 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.569A pdb=" N GLY B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 598 through 617 removed outlier: 4.021A pdb=" N GLY B 602 " --> pdb=" O GLY B 598 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 624 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.795A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.729A pdb=" N GLY B 689 " --> pdb=" O THR B 685 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.850A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 752 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 817 removed outlier: 3.586A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 804 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 813 " --> pdb=" O VAL B 809 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1028 removed outlier: 3.536A pdb=" N LEU B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B1013 " --> pdb=" O MET B1009 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B1014 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR B1024 " --> pdb=" O PHE B1020 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1102 Processing helix chain 'B' and resid 1104 through 1121 removed outlier: 3.800A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1122 through 1125 removed outlier: 3.768A pdb=" N GLU B1125 " --> pdb=" O ALA B1122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1122 through 1125' Processing helix chain 'B' and resid 1132 through 1161 removed outlier: 3.555A pdb=" N SER B1136 " --> pdb=" O ASN B1132 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B1138 " --> pdb=" O ILE B1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B1139 " --> pdb=" O LEU B1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B1140 " --> pdb=" O SER B1136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B1160 " --> pdb=" O ILE B1156 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1209 removed outlier: 4.277A pdb=" N GLY B1182 " --> pdb=" O SER B1178 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B1183 " --> pdb=" O PHE B1179 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B1187 " --> pdb=" O ALA B1183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B1188 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B1190 " --> pdb=" O PHE B1186 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY B1193 " --> pdb=" O ALA B1189 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU B1195 " --> pdb=" O MET B1191 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.634A pdb=" N SER C 37 " --> pdb=" O MET C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 removed outlier: 4.078A pdb=" N THR C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 139 through 142 Processing helix chain 'C' and resid 143 through 156 removed outlier: 3.625A pdb=" N LEU C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.717A pdb=" N LYS C 172 " --> pdb=" O ASN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.923A pdb=" N ARG C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 4.196A pdb=" N ASP C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.688A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.770A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.620A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 430 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 3.811A pdb=" N LEU C 467 " --> pdb=" O MET C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.642A pdb=" N TRP C 526 " --> pdb=" O ALA C 522 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N MET C 527 " --> pdb=" O TYR C 523 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE C 531 " --> pdb=" O MET C 527 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.849A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 624 removed outlier: 3.649A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 613 " --> pdb=" O THR C 609 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 642 Processing helix chain 'C' and resid 653 through 662 removed outlier: 3.796A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.728A pdb=" N GLY C 689 " --> pdb=" O THR C 685 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.849A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS C 752 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 753 " --> pdb=" O ALA C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 768 Processing helix chain 'C' and resid 789 through 791 No H-bonds generated for 'chain 'C' and resid 789 through 791' Processing helix chain 'C' and resid 792 through 820 removed outlier: 4.184A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 810 " --> pdb=" O ALA C 806 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C 820 " --> pdb=" O TYR C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1028 removed outlier: 3.537A pdb=" N LEU C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C1013 " --> pdb=" O MET C1009 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C1014 " --> pdb=" O LEU C1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR C1024 " --> pdb=" O PHE C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1102 Processing helix chain 'C' and resid 1104 through 1121 removed outlier: 3.799A pdb=" N LEU C1114 " --> pdb=" O SER C1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 1122 through 1125 removed outlier: 3.768A pdb=" N GLU C1125 " --> pdb=" O ALA C1122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1122 through 1125' Processing helix chain 'C' and resid 1132 through 1161 removed outlier: 3.555A pdb=" N SER C1136 " --> pdb=" O ASN C1132 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C1138 " --> pdb=" O ILE C1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C1141 " --> pdb=" O ALA C1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C1160 " --> pdb=" O ILE C1156 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1209 removed outlier: 4.277A pdb=" N GLY C1182 " --> pdb=" O SER C1178 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA C1183 " --> pdb=" O PHE C1179 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C1187 " --> pdb=" O ALA C1183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C1188 " --> pdb=" O LEU C1184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C1190 " --> pdb=" O PHE C1186 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C1193 " --> pdb=" O ALA C1189 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU C1195 " --> pdb=" O MET C1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.635A pdb=" N SER D 37 " --> pdb=" O MET D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 69 Processing helix chain 'D' and resid 81 through 93 removed outlier: 4.078A pdb=" N THR D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 139 through 142 Processing helix chain 'D' and resid 143 through 156 removed outlier: 3.625A pdb=" N LEU D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 173 removed outlier: 3.718A pdb=" N LYS D 172 " --> pdb=" O ASN D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.922A pdb=" N ARG D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 removed outlier: 4.196A pdb=" N ASP D 206 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.688A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.770A pdb=" N VAL D 289 " --> pdb=" O THR D 285 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.620A pdb=" N ASP D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 removed outlier: 3.811A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 519 removed outlier: 3.518A pdb=" N SER D 516 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE D 517 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 544 removed outlier: 3.569A pdb=" N GLY D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 598 through 617 removed outlier: 4.022A pdb=" N GLY D 602 " --> pdb=" O GLY D 598 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 603 " --> pdb=" O ARG D 599 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 624 Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.796A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.729A pdb=" N GLY D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.849A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS D 752 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 753 " --> pdb=" O ALA D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 774 through 779 Processing helix chain 'D' and resid 788 through 792 Processing helix chain 'D' and resid 793 through 817 removed outlier: 3.586A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 804 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 805 " --> pdb=" O GLY D 801 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 812 " --> pdb=" O LEU D 808 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 813 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS D 815 " --> pdb=" O LEU D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1028 removed outlier: 3.537A pdb=" N LEU D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR D1013 " --> pdb=" O MET D1009 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D1014 " --> pdb=" O LEU D1010 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D1024 " --> pdb=" O PHE D1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1102 Processing helix chain 'D' and resid 1104 through 1121 removed outlier: 3.800A pdb=" N LEU D1114 " --> pdb=" O SER D1110 " (cutoff:3.500A) Processing helix chain 'D' and resid 1122 through 1125 removed outlier: 3.767A pdb=" N GLU D1125 " --> pdb=" O ALA D1122 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1122 through 1125' Processing helix chain 'D' and resid 1132 through 1161 removed outlier: 3.555A pdb=" N SER D1136 " --> pdb=" O ASN D1132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY D1138 " --> pdb=" O ILE D1134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D1139 " --> pdb=" O LEU D1135 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D1140 " --> pdb=" O SER D1136 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D1151 " --> pdb=" O SER D1147 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D1160 " --> pdb=" O ILE D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1209 removed outlier: 4.277A pdb=" N GLY D1182 " --> pdb=" O SER D1178 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA D1183 " --> pdb=" O PHE D1179 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D1187 " --> pdb=" O ALA D1183 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D1188 " --> pdb=" O LEU D1184 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D1190 " --> pdb=" O PHE D1186 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY D1193 " --> pdb=" O ALA D1189 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 49 removed outlier: 3.604A pdb=" N HIS A 46 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 72 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 5.412A pdb=" N ARG A 191 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 372 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 347 Processing sheet with id=AA5, first strand: chain 'A' and resid 394 through 399 removed outlier: 5.901A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA8, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.813A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.047A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 10.307A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1065 through 1067 removed outlier: 3.724A pdb=" N CYS A1066 " --> pdb=" O HIS A1059 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A1035 " --> pdb=" O THR A1058 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 49 removed outlier: 3.604A pdb=" N HIS B 46 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 72 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 164 removed outlier: 5.413A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE B 245 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AB5, first strand: chain 'B' and resid 346 through 347 Processing sheet with id=AB6, first strand: chain 'B' and resid 394 through 399 removed outlier: 5.934A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B 443 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.814A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.049A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1065 through 1067 removed outlier: 3.725A pdb=" N CYS B1066 " --> pdb=" O HIS B1059 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B1035 " --> pdb=" O THR B1058 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 42 through 49 removed outlier: 3.603A pdb=" N HIS C 46 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 72 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 159 through 164 removed outlier: 5.413A pdb=" N ARG C 191 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY C 372 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AC6, first strand: chain 'C' and resid 346 through 347 Processing sheet with id=AC7, first strand: chain 'C' and resid 394 through 399 removed outlier: 5.967A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AC9, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AD1, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.813A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 646 through 648 removed outlier: 6.048A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1065 through 1067 removed outlier: 3.725A pdb=" N CYS C1066 " --> pdb=" O HIS C1059 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C1035 " --> pdb=" O THR C1058 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 42 through 49 removed outlier: 3.604A pdb=" N HIS D 46 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 159 through 164 removed outlier: 5.411A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N PHE D 245 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AD7, first strand: chain 'D' and resid 346 through 347 Processing sheet with id=AD8, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.131A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AE1, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AE2, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.814A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.048A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1065 through 1067 removed outlier: 3.724A pdb=" N CYS D1066 " --> pdb=" O HIS D1059 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D1035 " --> pdb=" O THR D1058 " (cutoff:3.500A) 1390 hydrogen bonds defined for protein. 4020 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: 6.25 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 5083 1.27 - 1.41: 8151 1.41 - 1.55: 18308 1.55 - 1.69: 18 1.69 - 1.83: 280 Bond restraints: 31840 Sorted by residual: bond pdb=" C3 CYZ A1302 " pdb=" C4 CYZ A1302 " ideal model delta sigma weight residual 1.334 1.125 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C3 CYZ B1302 " pdb=" C4 CYZ B1302 " ideal model delta sigma weight residual 1.334 1.125 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C3 CYZ C1302 " pdb=" C4 CYZ C1302 " ideal model delta sigma weight residual 1.334 1.126 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C3 CYZ D1302 " pdb=" C4 CYZ D1302 " ideal model delta sigma weight residual 1.334 1.126 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C1 CYZ A1302 " pdb=" C6 CYZ A1302 " ideal model delta sigma weight residual 1.553 1.755 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 31835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 42553 3.60 - 7.21: 432 7.21 - 10.81: 42 10.81 - 14.41: 3 14.41 - 18.01: 4 Bond angle restraints: 43034 Sorted by residual: angle pdb=" N GLU B 384 " pdb=" CA GLU B 384 " pdb=" C GLU B 384 " ideal model delta sigma weight residual 110.91 120.45 -9.54 1.17e+00 7.31e-01 6.65e+01 angle pdb=" N GLU D 384 " pdb=" CA GLU D 384 " pdb=" C GLU D 384 " ideal model delta sigma weight residual 110.91 120.44 -9.53 1.17e+00 7.31e-01 6.63e+01 angle pdb=" O3 CYZ C1302 " pdb=" S2 CYZ C1302 " pdb=" O4 CYZ C1302 " ideal model delta sigma weight residual 118.35 100.34 18.01 3.00e+00 1.11e-01 3.61e+01 angle pdb=" O3 CYZ A1302 " pdb=" S2 CYZ A1302 " pdb=" O4 CYZ A1302 " ideal model delta sigma weight residual 118.35 101.23 17.12 3.00e+00 1.11e-01 3.26e+01 angle pdb=" O3 CYZ B1302 " pdb=" S2 CYZ B1302 " pdb=" O4 CYZ B1302 " ideal model delta sigma weight residual 118.35 101.31 17.04 3.00e+00 1.11e-01 3.22e+01 ... (remaining 43029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 18333 21.47 - 42.93: 408 42.93 - 64.40: 23 64.40 - 85.87: 10 85.87 - 107.34: 4 Dihedral angle restraints: 18778 sinusoidal: 7420 harmonic: 11358 Sorted by residual: dihedral pdb=" CA SER D 635 " pdb=" C SER D 635 " pdb=" N ALA D 636 " pdb=" CA ALA D 636 " ideal model delta harmonic sigma weight residual -180.00 -126.33 -53.67 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA SER B 635 " pdb=" C SER B 635 " pdb=" N ALA B 636 " pdb=" CA ALA B 636 " ideal model delta harmonic sigma weight residual -180.00 -126.33 -53.67 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CA SER C 635 " pdb=" C SER C 635 " pdb=" N ALA C 636 " pdb=" CA ALA C 636 " ideal model delta harmonic sigma weight residual 180.00 -126.34 -53.66 0 5.00e+00 4.00e-02 1.15e+02 ... (remaining 18775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 4691 0.146 - 0.293: 75 0.293 - 0.439: 0 0.439 - 0.585: 0 0.585 - 0.731: 8 Chirality restraints: 4774 Sorted by residual: chirality pdb=" C2 CYZ C1302 " pdb=" C1 CYZ C1302 " pdb=" C3 CYZ C1302 " pdb=" C7 CYZ C1302 " both_signs ideal model delta sigma weight residual False 3.31 2.58 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C2 CYZ D1302 " pdb=" C1 CYZ D1302 " pdb=" C3 CYZ D1302 " pdb=" C7 CYZ D1302 " both_signs ideal model delta sigma weight residual False 3.31 2.58 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C2 CYZ B1302 " pdb=" C1 CYZ B1302 " pdb=" C3 CYZ B1302 " pdb=" C7 CYZ B1302 " both_signs ideal model delta sigma weight residual False 3.31 2.58 0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 4771 not shown) Planarity restraints: 5408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.060 5.00e-02 4.00e+02 9.22e-02 1.36e+01 pdb=" N PRO D 99 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.060 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO A 99 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 98 " -0.060 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO B 99 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.049 5.00e-02 4.00e+02 ... (remaining 5405 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2719 2.73 - 3.27: 32386 3.27 - 3.82: 53537 3.82 - 4.36: 63692 4.36 - 4.90: 99427 Nonbonded interactions: 251761 Sorted by model distance: nonbonded pdb=" OG SER A 87 " pdb=" OD1 ASN B 54 " model vdw 2.188 3.040 nonbonded pdb=" O TYR A1031 " pdb=" OG SER A1178 " model vdw 2.218 3.040 nonbonded pdb=" O TYR D1031 " pdb=" OG SER D1178 " model vdw 2.219 3.040 nonbonded pdb=" O TYR C1031 " pdb=" OG SER C1178 " model vdw 2.219 3.040 nonbonded pdb=" O TYR B1031 " pdb=" OG SER B1178 " model vdw 2.219 3.040 ... (remaining 251756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1002 through 13 \ 02)) selection = (chain 'B' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 1302)) selection = (chain 'C' and (resid 10 through 504 or (resid 505 and (name N or name CA or nam \ e C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1002 through 13 \ 02)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.950 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 0.209 31856 Z= 0.458 Angle : 1.054 18.015 43066 Z= 0.581 Chirality : 0.061 0.731 4774 Planarity : 0.007 0.092 5408 Dihedral : 9.879 107.337 11478 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.26 % Favored : 92.69 % Rotamer: Outliers : 0.24 % Allowed : 2.43 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.69 (0.11), residues: 3910 helix: -2.75 (0.09), residues: 1620 sheet: -2.45 (0.26), residues: 408 loop : -2.04 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 453 TYR 0.028 0.003 TYR A 218 PHE 0.027 0.003 PHE B1072 TRP 0.029 0.004 TRP A 130 HIS 0.014 0.005 HIS C 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.46 (31840) covalent geometry : angle 1.05301 / 0.58 (43034) SS BOND : bond 0.00352 / 0.24 ( 16) SS BOND : angle 1.65641 / 1.21 ( 32) hydrogen bonds : bond 0.29914 / 19.80 ( 1390) hydrogen bonds : angle 9.63740 / 6.66 ( 4020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 766 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASP cc_start: 0.9275 (m-30) cc_final: 0.8754 (t70) REVERT: A 182 GLN cc_start: 0.8632 (mt0) cc_final: 0.8232 (tp40) REVERT: A 331 ARG cc_start: 0.9118 (ttt-90) cc_final: 0.8916 (ptm160) REVERT: A 369 ARG cc_start: 0.7814 (ptm160) cc_final: 0.7523 (ttm-80) REVERT: A 427 ASP cc_start: 0.8518 (m-30) cc_final: 0.8309 (m-30) REVERT: A 527 MET cc_start: 0.8880 (ttt) cc_final: 0.8355 (tpt) REVERT: A 651 ASP cc_start: 0.7216 (m-30) cc_final: 0.6534 (m-30) REVERT: A 1022 LEU cc_start: 0.8118 (mt) cc_final: 0.7835 (tp) REVERT: A 1082 PHE cc_start: 0.7693 (p90) cc_final: 0.6204 (t80) REVERT: B 18 PHE cc_start: 0.8968 (m-80) cc_final: 0.8514 (m-80) REVERT: B 73 ILE cc_start: 0.8825 (mt) cc_final: 0.8152 (mt) REVERT: B 113 MET cc_start: 0.8074 (mmp) cc_final: 0.7525 (mpp) REVERT: B 159 GLN cc_start: 0.7958 (mt0) cc_final: 0.7723 (mp10) REVERT: B 167 ASN cc_start: 0.7917 (m-40) cc_final: 0.7691 (p0) REVERT: B 408 MET cc_start: 0.8990 (mmm) cc_final: 0.8692 (mmm) REVERT: B 414 MET cc_start: 0.8183 (mtm) cc_final: 0.7782 (ptp) REVERT: B 415 LEU cc_start: 0.6486 (mt) cc_final: 0.5540 (mm) REVERT: B 549 TYR cc_start: 0.7766 (p90) cc_final: 0.7418 (p90) REVERT: B 813 GLU cc_start: 0.8582 (tt0) cc_final: 0.8078 (mm-30) REVERT: B 814 PHE cc_start: 0.8676 (t80) cc_final: 0.8380 (t80) REVERT: B 1027 VAL cc_start: 0.8776 (t) cc_final: 0.8381 (m) REVERT: B 1064 ARG cc_start: 0.7610 (mtm-85) cc_final: 0.7369 (mmt180) REVERT: B 1202 ASP cc_start: 0.8838 (m-30) cc_final: 0.8073 (t0) REVERT: C 171 ASP cc_start: 0.9163 (m-30) cc_final: 0.8757 (t0) REVERT: C 187 LYS cc_start: 0.9070 (mttt) cc_final: 0.8793 (mtmm) REVERT: C 304 ILE cc_start: 0.8613 (mt) cc_final: 0.7872 (tt) REVERT: C 369 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7078 (ttm-80) REVERT: C 414 MET cc_start: 0.8488 (mtm) cc_final: 0.8215 (tpp) REVERT: C 527 MET cc_start: 0.8634 (ttt) cc_final: 0.8260 (tpt) REVERT: C 570 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8504 (mp0) REVERT: C 1009 MET cc_start: 0.8235 (tpt) cc_final: 0.7805 (mtp) REVERT: C 1022 LEU cc_start: 0.7987 (mt) cc_final: 0.7754 (tp) REVERT: D 18 PHE cc_start: 0.9012 (m-80) cc_final: 0.8734 (m-80) REVERT: D 73 ILE cc_start: 0.8957 (mt) cc_final: 0.8262 (mt) REVERT: D 113 MET cc_start: 0.8378 (mmp) cc_final: 0.7986 (mpp) REVERT: D 159 GLN cc_start: 0.8342 (mt0) cc_final: 0.7915 (mp10) REVERT: D 265 LEU cc_start: 0.6326 (mt) cc_final: 0.6004 (mt) REVERT: D 519 ASP cc_start: 0.8129 (t0) cc_final: 0.7706 (t70) REVERT: D 541 PHE cc_start: 0.9368 (t80) cc_final: 0.9028 (t80) REVERT: D 573 ILE cc_start: 0.8981 (tp) cc_final: 0.8639 (tp) REVERT: D 670 MET cc_start: 0.9155 (mtp) cc_final: 0.8951 (mmm) REVERT: D 797 TYR cc_start: 0.8680 (m-10) cc_final: 0.8460 (m-10) REVERT: D 813 GLU cc_start: 0.8921 (tt0) cc_final: 0.8293 (tm-30) REVERT: D 1022 LEU cc_start: 0.8395 (mt) cc_final: 0.8128 (tp) REVERT: D 1027 VAL cc_start: 0.8115 (t) cc_final: 0.7313 (m) REVERT: D 1202 ASP cc_start: 0.8893 (m-30) cc_final: 0.8241 (t0) outliers start: 8 outliers final: 0 residues processed: 769 average time/residue: 0.2068 time to fit residues: 247.1083 Evaluate side-chains 364 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN A1131 HIS A1132 ASN B 24 GLN B 298 ASN B 302 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 569 ASN B 586 GLN B 642 GLN ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1131 HIS B1132 ASN B1204 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN C 726 ASN C1131 HIS C1132 ASN D 24 GLN D 298 ASN D 302 GLN ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 569 ASN D 586 GLN D 642 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN D1159 ASN D1204 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.090287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071430 restraints weight = 107175.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.070878 restraints weight = 92994.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.071807 restraints weight = 73993.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.072091 restraints weight = 59991.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072288 restraints weight = 54794.127| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 31856 Z= 0.211 Angle : 0.667 8.014 43066 Z= 0.364 Chirality : 0.044 0.208 4774 Planarity : 0.005 0.062 5408 Dihedral : 6.042 77.713 4292 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.60 (0.13), residues: 3910 helix: -0.09 (0.11), residues: 1752 sheet: -1.66 (0.29), residues: 348 loop : -1.91 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 675 TYR 0.020 0.002 TYR D 523 PHE 0.019 0.002 PHE C 623 TRP 0.030 0.002 TRP C1032 HIS 0.014 0.002 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (31840) covalent geometry : angle 0.66588 / 0.36 (43034) SS BOND : bond 0.01512 / 1.01 ( 16) SS BOND : angle 1.63092 / 1.14 ( 32) hydrogen bonds : bond 0.04932 / 3.28 ( 1390) hydrogen bonds : angle 5.22806 / 3.63 ( 4020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.8702 (t0) cc_final: 0.8428 (t70) REVERT: A 113 MET cc_start: 0.8774 (mmm) cc_final: 0.8161 (mmm) REVERT: A 171 ASP cc_start: 0.8932 (m-30) cc_final: 0.8562 (t0) REVERT: A 182 GLN cc_start: 0.8802 (mt0) cc_final: 0.8110 (tp40) REVERT: A 450 TYR cc_start: 0.8488 (m-80) cc_final: 0.8219 (m-80) REVERT: A 519 ASP cc_start: 0.8516 (t0) cc_final: 0.8294 (t0) REVERT: A 585 MET cc_start: 0.8357 (mtt) cc_final: 0.8075 (mtt) REVERT: A 728 ASP cc_start: 0.7923 (p0) cc_final: 0.6892 (m-30) REVERT: A 1082 PHE cc_start: 0.7388 (p90) cc_final: 0.5990 (t80) REVERT: B 406 VAL cc_start: 0.8606 (t) cc_final: 0.8107 (t) REVERT: B 503 MET cc_start: 0.8258 (tmm) cc_final: 0.7791 (tmm) REVERT: B 527 MET cc_start: 0.8267 (tpp) cc_final: 0.8002 (tpp) REVERT: B 816 TYR cc_start: 0.7884 (t80) cc_final: 0.7615 (t80) REVERT: B 1022 LEU cc_start: 0.9252 (tp) cc_final: 0.8991 (tp) REVERT: B 1064 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7492 (mmt180) REVERT: C 78 ASP cc_start: 0.8539 (t0) cc_final: 0.8252 (t70) REVERT: C 113 MET cc_start: 0.8718 (mmm) cc_final: 0.8274 (mmm) REVERT: C 171 ASP cc_start: 0.8738 (m-30) cc_final: 0.8370 (t0) REVERT: C 541 PHE cc_start: 0.8462 (t80) cc_final: 0.8216 (t80) REVERT: C 1010 LEU cc_start: 0.8344 (mt) cc_final: 0.8076 (mp) REVERT: C 1190 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8645 (mp0) REVERT: D 358 ILE cc_start: 0.9043 (mm) cc_final: 0.8730 (mm) REVERT: D 503 MET cc_start: 0.8113 (tmm) cc_final: 0.7656 (tmm) REVERT: D 527 MET cc_start: 0.8190 (tpp) cc_final: 0.7895 (tpp) REVERT: D 541 PHE cc_start: 0.9064 (t80) cc_final: 0.8847 (t80) REVERT: D 1064 ARG cc_start: 0.7297 (mpt180) cc_final: 0.6893 (mmt180) REVERT: D 1149 ILE cc_start: 0.9088 (tt) cc_final: 0.8789 (tp) REVERT: D 1202 ASP cc_start: 0.8773 (m-30) cc_final: 0.8059 (t0) outliers start: 1 outliers final: 1 residues processed: 461 average time/residue: 0.1792 time to fit residues: 134.8083 Evaluate side-chains 273 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 196 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 359 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 225 optimal weight: 0.4980 chunk 206 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1204 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 642 GLN D 791 ASN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.088814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069159 restraints weight = 107252.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069297 restraints weight = 83095.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069773 restraints weight = 68073.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.070053 restraints weight = 58067.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.070183 restraints weight = 54392.995| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31856 Z= 0.174 Angle : 0.593 8.256 43066 Z= 0.317 Chirality : 0.042 0.174 4774 Planarity : 0.005 0.065 5408 Dihedral : 5.612 78.262 4292 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.76 (0.13), residues: 3910 helix: 0.93 (0.12), residues: 1790 sheet: -1.66 (0.27), residues: 382 loop : -1.80 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 675 TYR 0.024 0.002 TYR D 647 PHE 0.024 0.002 PHE C 546 TRP 0.017 0.001 TRP C1032 HIS 0.006 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (31840) covalent geometry : angle 0.59193 / 0.32 (43034) SS BOND : bond 0.00567 / 0.38 ( 16) SS BOND : angle 1.53906 / 1.03 ( 32) hydrogen bonds : bond 0.04141 / 2.72 ( 1390) hydrogen bonds : angle 4.81047 / 3.34 ( 4020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8894 (mmm) cc_final: 0.7899 (mmm) REVERT: A 171 ASP cc_start: 0.8427 (m-30) cc_final: 0.8217 (t0) REVERT: A 450 TYR cc_start: 0.8502 (m-80) cc_final: 0.8166 (m-80) REVERT: A 585 MET cc_start: 0.8293 (mtt) cc_final: 0.7982 (mtt) REVERT: A 688 GLU cc_start: 0.8293 (tt0) cc_final: 0.7657 (tm-30) REVERT: A 728 ASP cc_start: 0.8250 (p0) cc_final: 0.7209 (m-30) REVERT: B 113 MET cc_start: 0.8903 (mpp) cc_final: 0.8484 (mpp) REVERT: B 503 MET cc_start: 0.8141 (tmm) cc_final: 0.7431 (tmm) REVERT: B 1009 MET cc_start: 0.8789 (tpp) cc_final: 0.8255 (tpp) REVERT: B 1022 LEU cc_start: 0.9325 (tp) cc_final: 0.9016 (tp) REVERT: B 1191 MET cc_start: 0.8111 (tpt) cc_final: 0.7669 (tpp) REVERT: C 113 MET cc_start: 0.8853 (mmm) cc_final: 0.8020 (mmm) REVERT: C 171 ASP cc_start: 0.8579 (m-30) cc_final: 0.8229 (t0) REVERT: C 265 LEU cc_start: 0.7909 (mt) cc_final: 0.7651 (mt) REVERT: C 708 MET cc_start: 0.7931 (mmt) cc_final: 0.7546 (tpp) REVERT: C 1010 LEU cc_start: 0.8189 (mt) cc_final: 0.7935 (mp) REVERT: C 1022 LEU cc_start: 0.8283 (tp) cc_final: 0.8066 (tp) REVERT: D 113 MET cc_start: 0.8944 (mpp) cc_final: 0.8506 (mpp) REVERT: D 299 LEU cc_start: 0.8120 (tp) cc_final: 0.7632 (mt) REVERT: D 358 ILE cc_start: 0.8987 (mm) cc_final: 0.8750 (mm) REVERT: D 456 ASP cc_start: 0.7864 (m-30) cc_final: 0.7378 (t0) REVERT: D 503 MET cc_start: 0.8297 (tmm) cc_final: 0.7663 (tmm) REVERT: D 1022 LEU cc_start: 0.9443 (tp) cc_final: 0.9232 (tp) REVERT: D 1149 ILE cc_start: 0.9092 (tt) cc_final: 0.8807 (tp) REVERT: D 1202 ASP cc_start: 0.8708 (m-30) cc_final: 0.8192 (t0) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1723 time to fit residues: 109.2346 Evaluate side-chains 250 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 379 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 236 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 308 optimal weight: 0.2980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.090285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.070062 restraints weight = 104767.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.070731 restraints weight = 73955.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071138 restraints weight = 57321.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071320 restraints weight = 52371.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.071722 restraints weight = 49819.494| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 31856 Z= 0.112 Angle : 0.516 6.108 43066 Z= 0.277 Chirality : 0.040 0.159 4774 Planarity : 0.004 0.054 5408 Dihedral : 5.209 73.379 4292 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.25 (0.13), residues: 3910 helix: 1.40 (0.12), residues: 1798 sheet: -1.16 (0.29), residues: 328 loop : -1.67 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 453 TYR 0.015 0.001 TYR D 673 PHE 0.020 0.001 PHE C 546 TRP 0.022 0.001 TRP A 323 HIS 0.014 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (31840) covalent geometry : angle 0.51524 / 0.28 (43034) SS BOND : bond 0.00571 / 0.39 ( 16) SS BOND : angle 1.36191 / 0.96 ( 32) hydrogen bonds : bond 0.03265 / 2.16 ( 1390) hydrogen bonds : angle 4.36422 / 3.03 ( 4020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 1.240 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: A 113 MET cc_start: 0.8753 (mmm) cc_final: 0.8101 (mmm) REVERT: A 585 MET cc_start: 0.8427 (mtt) cc_final: 0.8205 (mtt) REVERT: A 639 LEU cc_start: 0.7775 (mp) cc_final: 0.7509 (mp) REVERT: A 688 GLU cc_start: 0.8385 (tt0) cc_final: 0.7638 (tm-30) REVERT: A 728 ASP cc_start: 0.8169 (p0) cc_final: 0.7027 (m-30) REVERT: A 1082 PHE cc_start: 0.7124 (p90) cc_final: 0.5947 (t80) REVERT: B 113 MET cc_start: 0.8917 (mpp) cc_final: 0.8163 (mpp) REVERT: B 503 MET cc_start: 0.8350 (tmm) cc_final: 0.7648 (tmm) REVERT: B 519 ASP cc_start: 0.8135 (t70) cc_final: 0.7237 (t0) REVERT: B 1009 MET cc_start: 0.8549 (tpp) cc_final: 0.8034 (tpp) REVERT: B 1022 LEU cc_start: 0.9293 (tp) cc_final: 0.8993 (tp) REVERT: B 1116 MET cc_start: 0.8746 (ttm) cc_final: 0.8503 (ttm) REVERT: B 1149 ILE cc_start: 0.9148 (tt) cc_final: 0.8908 (tp) REVERT: B 1191 MET cc_start: 0.8033 (tpt) cc_final: 0.7688 (tpp) REVERT: B 1202 ASP cc_start: 0.8679 (m-30) cc_final: 0.8205 (t0) REVERT: C 85 ILE cc_start: 0.9057 (mm) cc_final: 0.8661 (tt) REVERT: C 113 MET cc_start: 0.8796 (mmm) cc_final: 0.7713 (mmm) REVERT: C 171 ASP cc_start: 0.8470 (m-30) cc_final: 0.8128 (t0) REVERT: C 541 PHE cc_start: 0.8431 (t80) cc_final: 0.8205 (t80) REVERT: C 639 LEU cc_start: 0.7940 (mp) cc_final: 0.7604 (mp) REVERT: C 688 GLU cc_start: 0.8262 (tt0) cc_final: 0.8027 (tp30) REVERT: C 702 TYR cc_start: 0.8356 (t80) cc_final: 0.8146 (t80) REVERT: C 708 MET cc_start: 0.7968 (mmt) cc_final: 0.7505 (tpp) REVERT: C 769 ASP cc_start: 0.8193 (m-30) cc_final: 0.7989 (t70) REVERT: C 1022 LEU cc_start: 0.8228 (tp) cc_final: 0.7969 (tp) REVERT: D 113 MET cc_start: 0.9027 (mpp) cc_final: 0.8174 (mpp) REVERT: D 456 ASP cc_start: 0.7864 (m-30) cc_final: 0.7350 (t0) REVERT: D 503 MET cc_start: 0.8308 (tmm) cc_final: 0.7623 (tmm) REVERT: D 519 ASP cc_start: 0.8157 (t70) cc_final: 0.7294 (t70) REVERT: D 1022 LEU cc_start: 0.9332 (tp) cc_final: 0.9012 (tp) REVERT: D 1149 ILE cc_start: 0.9214 (tt) cc_final: 0.8989 (tp) REVERT: D 1184 LEU cc_start: 0.9446 (tp) cc_final: 0.9162 (tt) REVERT: D 1191 MET cc_start: 0.7954 (tpt) cc_final: 0.7613 (tpp) REVERT: D 1202 ASP cc_start: 0.8663 (m-30) cc_final: 0.8162 (t0) outliers start: 0 outliers final: 0 residues processed: 394 average time/residue: 0.1852 time to fit residues: 120.2857 Evaluate side-chains 253 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 120 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 389 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 241 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 237 optimal weight: 0.8980 chunk 377 optimal weight: 0.9980 chunk 350 optimal weight: 0.0050 chunk 347 optimal weight: 0.9980 chunk 357 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.090662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.071616 restraints weight = 105729.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.071734 restraints weight = 78362.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072071 restraints weight = 66176.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.072345 restraints weight = 57205.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.072504 restraints weight = 53291.765| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 31856 Z= 0.100 Angle : 0.507 7.888 43066 Z= 0.270 Chirality : 0.040 0.157 4774 Planarity : 0.004 0.058 5408 Dihedral : 4.966 72.817 4292 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.04 (0.14), residues: 3910 helix: 1.65 (0.12), residues: 1798 sheet: -1.05 (0.28), residues: 340 loop : -1.52 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 309 TYR 0.025 0.001 TYR D 523 PHE 0.020 0.001 PHE C 546 TRP 0.028 0.001 TRP C1032 HIS 0.010 0.001 HIS B1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (31840) covalent geometry : angle 0.50625 / 0.27 (43034) SS BOND : bond 0.00789 / 0.55 ( 16) SS BOND : angle 1.28145 / 0.84 ( 32) hydrogen bonds : bond 0.02976 / 1.96 ( 1390) hydrogen bonds : angle 4.16768 / 2.90 ( 4020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8779 (mmm) cc_final: 0.8117 (mmm) REVERT: A 585 MET cc_start: 0.8401 (mtt) cc_final: 0.8162 (mtt) REVERT: A 639 LEU cc_start: 0.7672 (mp) cc_final: 0.7372 (mp) REVERT: A 702 TYR cc_start: 0.8168 (t80) cc_final: 0.7963 (t80) REVERT: A 728 ASP cc_start: 0.8004 (p0) cc_final: 0.7031 (m-30) REVERT: A 1082 PHE cc_start: 0.7168 (p90) cc_final: 0.6016 (t80) REVERT: B 55 SER cc_start: 0.9311 (m) cc_final: 0.9101 (p) REVERT: B 113 MET cc_start: 0.9013 (mpp) cc_final: 0.8420 (mpp) REVERT: B 503 MET cc_start: 0.8312 (tmm) cc_final: 0.7752 (tmm) REVERT: B 1009 MET cc_start: 0.8629 (tpp) cc_final: 0.8272 (tpp) REVERT: B 1022 LEU cc_start: 0.9375 (tp) cc_final: 0.9121 (tp) REVERT: B 1116 MET cc_start: 0.8745 (ttm) cc_final: 0.8463 (ttm) REVERT: B 1149 ILE cc_start: 0.9079 (tt) cc_final: 0.8862 (tp) REVERT: B 1191 MET cc_start: 0.8109 (tpt) cc_final: 0.7725 (tpp) REVERT: B 1195 LEU cc_start: 0.9218 (mm) cc_final: 0.8995 (mm) REVERT: B 1202 ASP cc_start: 0.8749 (m-30) cc_final: 0.8276 (t0) REVERT: C 85 ILE cc_start: 0.9045 (mm) cc_final: 0.8679 (tt) REVERT: C 113 MET cc_start: 0.8765 (mmm) cc_final: 0.8255 (mmm) REVERT: C 171 ASP cc_start: 0.8617 (m-30) cc_final: 0.8229 (t0) REVERT: C 450 TYR cc_start: 0.8616 (m-10) cc_final: 0.8401 (m-80) REVERT: C 541 PHE cc_start: 0.8394 (t80) cc_final: 0.8157 (t80) REVERT: C 639 LEU cc_start: 0.8069 (mp) cc_final: 0.7651 (mp) REVERT: C 688 GLU cc_start: 0.8370 (tt0) cc_final: 0.8137 (tp30) REVERT: C 702 TYR cc_start: 0.8292 (t80) cc_final: 0.8060 (t80) REVERT: C 708 MET cc_start: 0.7601 (mmt) cc_final: 0.7276 (tpp) REVERT: C 769 ASP cc_start: 0.8302 (m-30) cc_final: 0.8047 (t70) REVERT: D 113 MET cc_start: 0.9009 (mpp) cc_final: 0.8349 (mpp) REVERT: D 456 ASP cc_start: 0.7987 (m-30) cc_final: 0.7425 (t0) REVERT: D 503 MET cc_start: 0.8316 (tmm) cc_final: 0.7472 (tmm) REVERT: D 1159 ASN cc_start: 0.8486 (t0) cc_final: 0.7904 (m110) REVERT: D 1202 ASP cc_start: 0.8716 (m-30) cc_final: 0.8216 (t0) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.1706 time to fit residues: 105.8443 Evaluate side-chains 254 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 49 optimal weight: 0.0770 chunk 16 optimal weight: 0.0980 chunk 326 optimal weight: 6.9990 chunk 380 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 387 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN B1204 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.090689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.070458 restraints weight = 105286.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071656 restraints weight = 75375.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.071818 restraints weight = 55994.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.072023 restraints weight = 53066.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072101 restraints weight = 51027.559| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31856 Z= 0.099 Angle : 0.502 6.508 43066 Z= 0.267 Chirality : 0.039 0.157 4774 Planarity : 0.004 0.051 5408 Dihedral : 4.858 72.309 4292 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.24 (0.14), residues: 3910 helix: 1.82 (0.12), residues: 1802 sheet: -1.02 (0.28), residues: 346 loop : -1.42 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1101 TYR 0.026 0.001 TYR B 523 PHE 0.021 0.001 PHE C 546 TRP 0.037 0.001 TRP A1032 HIS 0.004 0.001 HIS C1131 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (31840) covalent geometry : angle 0.50119 / 0.27 (43034) SS BOND : bond 0.00535 / 0.36 ( 16) SS BOND : angle 1.36443 / 0.98 ( 32) hydrogen bonds : bond 0.02875 / 1.88 ( 1390) hydrogen bonds : angle 4.09447 / 2.85 ( 4020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.209 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: A 54 ASN cc_start: 0.8420 (t0) cc_final: 0.8061 (t0) REVERT: A 113 MET cc_start: 0.8802 (mmm) cc_final: 0.8094 (mmm) REVERT: A 639 LEU cc_start: 0.7644 (mp) cc_final: 0.7173 (mp) REVERT: A 728 ASP cc_start: 0.8053 (p0) cc_final: 0.7134 (m-30) REVERT: A 805 LEU cc_start: 0.9279 (tt) cc_final: 0.9036 (tt) REVERT: A 1082 PHE cc_start: 0.7200 (p90) cc_final: 0.6019 (t80) REVERT: B 113 MET cc_start: 0.9047 (mpp) cc_final: 0.8426 (mpp) REVERT: B 407 MET cc_start: 0.8449 (mmt) cc_final: 0.8097 (mmp) REVERT: B 503 MET cc_start: 0.8313 (tmm) cc_final: 0.7701 (tmm) REVERT: B 1057 MET cc_start: 0.6265 (mpp) cc_final: 0.5662 (mpp) REVERT: B 1116 MET cc_start: 0.8802 (ttm) cc_final: 0.8552 (ttm) REVERT: B 1149 ILE cc_start: 0.9089 (tt) cc_final: 0.8867 (tp) REVERT: B 1184 LEU cc_start: 0.9435 (tp) cc_final: 0.9131 (tt) REVERT: B 1191 MET cc_start: 0.8117 (tpt) cc_final: 0.7808 (tpp) REVERT: B 1202 ASP cc_start: 0.8765 (m-30) cc_final: 0.8251 (t0) REVERT: C 113 MET cc_start: 0.8804 (mmm) cc_final: 0.8040 (mmm) REVERT: C 171 ASP cc_start: 0.8528 (m-30) cc_final: 0.8171 (t0) REVERT: C 688 GLU cc_start: 0.8329 (tt0) cc_final: 0.8032 (tp30) REVERT: C 708 MET cc_start: 0.7668 (mmt) cc_final: 0.7381 (tpp) REVERT: C 769 ASP cc_start: 0.8262 (m-30) cc_final: 0.8043 (t70) REVERT: C 1190 GLU cc_start: 0.9012 (mp0) cc_final: 0.8435 (mp0) REVERT: D 113 MET cc_start: 0.9038 (mpp) cc_final: 0.8435 (mpp) REVERT: D 456 ASP cc_start: 0.7965 (m-30) cc_final: 0.7453 (t0) REVERT: D 503 MET cc_start: 0.8332 (tmm) cc_final: 0.7547 (tmm) REVERT: D 519 ASP cc_start: 0.8321 (t0) cc_final: 0.7859 (t0) REVERT: D 527 MET cc_start: 0.8040 (mmt) cc_final: 0.7735 (tpp) REVERT: D 1057 MET cc_start: 0.6333 (mpp) cc_final: 0.5661 (mpp) REVERT: D 1159 ASN cc_start: 0.8505 (t0) cc_final: 0.8014 (m-40) REVERT: D 1184 LEU cc_start: 0.9448 (tp) cc_final: 0.9162 (tp) REVERT: D 1202 ASP cc_start: 0.8695 (m-30) cc_final: 0.8132 (t0) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1647 time to fit residues: 98.6006 Evaluate side-chains 258 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 151 optimal weight: 5.9990 chunk 389 optimal weight: 1.9990 chunk 252 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 263 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 302 GLN B 337 GLN B1159 ASN B1204 HIS ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN D 569 ASN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1204 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.089782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.070513 restraints weight = 105440.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070697 restraints weight = 84478.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.071314 restraints weight = 66926.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071469 restraints weight = 57922.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.071670 restraints weight = 54476.540| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31856 Z= 0.119 Angle : 0.522 8.111 43066 Z= 0.276 Chirality : 0.040 0.159 4774 Planarity : 0.004 0.052 5408 Dihedral : 4.871 72.536 4292 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.03 % Allowed : 0.99 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.35 (0.14), residues: 3910 helix: 1.99 (0.13), residues: 1800 sheet: -0.95 (0.27), residues: 376 loop : -1.46 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1101 TYR 0.015 0.001 TYR C 702 PHE 0.025 0.001 PHE A 546 TRP 0.025 0.001 TRP C 323 HIS 0.015 0.001 HIS C1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (31840) covalent geometry : angle 0.52086 / 0.28 (43034) SS BOND : bond 0.00616 / 0.43 ( 16) SS BOND : angle 1.31861 / 0.92 ( 32) hydrogen bonds : bond 0.03057 / 2.02 ( 1390) hydrogen bonds : angle 4.12581 / 2.88 ( 4020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 0.949 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: A 54 ASN cc_start: 0.8317 (t0) cc_final: 0.8029 (t0) REVERT: A 113 MET cc_start: 0.8811 (mmm) cc_final: 0.8065 (mmm) REVERT: A 639 LEU cc_start: 0.7569 (mp) cc_final: 0.7135 (mp) REVERT: A 702 TYR cc_start: 0.8138 (t80) cc_final: 0.7932 (t80) REVERT: A 728 ASP cc_start: 0.7946 (p0) cc_final: 0.7087 (m-30) REVERT: A 1010 LEU cc_start: 0.8626 (mp) cc_final: 0.8303 (mm) REVERT: A 1082 PHE cc_start: 0.7248 (p90) cc_final: 0.6115 (t80) REVERT: B 113 MET cc_start: 0.9113 (mpp) cc_final: 0.8570 (mpp) REVERT: B 503 MET cc_start: 0.8293 (tmm) cc_final: 0.7501 (tmm) REVERT: B 527 MET cc_start: 0.8068 (mmt) cc_final: 0.7858 (tpp) REVERT: B 1057 MET cc_start: 0.6274 (mpp) cc_final: 0.5806 (mpp) REVERT: B 1116 MET cc_start: 0.8740 (ttm) cc_final: 0.8470 (ttm) REVERT: B 1184 LEU cc_start: 0.9415 (tp) cc_final: 0.9132 (tt) REVERT: B 1186 PHE cc_start: 0.8762 (t80) cc_final: 0.8483 (t80) REVERT: B 1191 MET cc_start: 0.8072 (tpt) cc_final: 0.7839 (tpp) REVERT: B 1202 ASP cc_start: 0.8687 (m-30) cc_final: 0.8286 (t0) REVERT: C 113 MET cc_start: 0.8770 (mmm) cc_final: 0.8196 (mmm) REVERT: C 171 ASP cc_start: 0.8483 (m-30) cc_final: 0.8218 (t0) REVERT: C 544 SER cc_start: 0.8664 (m) cc_final: 0.8210 (p) REVERT: C 688 GLU cc_start: 0.8414 (tt0) cc_final: 0.7622 (tm-30) REVERT: C 708 MET cc_start: 0.7550 (mmt) cc_final: 0.7239 (tpp) REVERT: C 769 ASP cc_start: 0.8246 (m-30) cc_final: 0.7950 (t70) REVERT: C 1190 GLU cc_start: 0.9028 (mp0) cc_final: 0.8501 (mp0) REVERT: D 113 MET cc_start: 0.9099 (mpp) cc_final: 0.8564 (mpp) REVERT: D 456 ASP cc_start: 0.8016 (m-30) cc_final: 0.7443 (t0) REVERT: D 503 MET cc_start: 0.8354 (tmm) cc_final: 0.7607 (tmm) REVERT: D 527 MET cc_start: 0.8115 (mmt) cc_final: 0.7728 (tpp) REVERT: D 1159 ASN cc_start: 0.8634 (t0) cc_final: 0.8160 (m110) REVERT: D 1202 ASP cc_start: 0.8671 (m-30) cc_final: 0.8237 (t0) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.1631 time to fit residues: 92.7983 Evaluate side-chains 242 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 15 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 373 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 330 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN B1159 ASN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.087901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.067334 restraints weight = 106564.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067997 restraints weight = 78963.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068180 restraints weight = 61632.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.068415 restraints weight = 59885.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068491 restraints weight = 55253.902| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31856 Z= 0.157 Angle : 0.573 11.184 43066 Z= 0.303 Chirality : 0.041 0.170 4774 Planarity : 0.004 0.051 5408 Dihedral : 5.020 73.750 4292 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.06 % Allowed : 0.54 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.33 (0.14), residues: 3910 helix: 2.00 (0.13), residues: 1792 sheet: -0.96 (0.28), residues: 362 loop : -1.48 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 599 TYR 0.015 0.001 TYR C 702 PHE 0.028 0.001 PHE A 546 TRP 0.023 0.001 TRP A1032 HIS 0.011 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (31840) covalent geometry : angle 0.57173 / 0.30 (43034) SS BOND : bond 0.00594 / 0.41 ( 16) SS BOND : angle 1.23419 / 0.86 ( 32) hydrogen bonds : bond 0.03463 / 2.28 ( 1390) hydrogen bonds : angle 4.29272 / 3.00 ( 4020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 316 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8897 (mmm) cc_final: 0.8134 (mmm) REVERT: A 544 SER cc_start: 0.8946 (m) cc_final: 0.8525 (p) REVERT: A 639 LEU cc_start: 0.7664 (mp) cc_final: 0.7235 (mp) REVERT: A 728 ASP cc_start: 0.8165 (p0) cc_final: 0.7214 (m-30) REVERT: A 805 LEU cc_start: 0.9254 (tt) cc_final: 0.9044 (tt) REVERT: A 1082 PHE cc_start: 0.7512 (p90) cc_final: 0.6256 (t80) REVERT: B 113 MET cc_start: 0.9081 (mpp) cc_final: 0.8569 (mpp) REVERT: B 407 MET cc_start: 0.8237 (mmt) cc_final: 0.7991 (mmp) REVERT: B 463 MET cc_start: 0.7910 (mpp) cc_final: 0.7670 (mmm) REVERT: B 503 MET cc_start: 0.8401 (tmm) cc_final: 0.7565 (tmm) REVERT: B 527 MET cc_start: 0.8176 (mmt) cc_final: 0.7786 (tpp) REVERT: B 1057 MET cc_start: 0.6467 (mpp) cc_final: 0.6106 (mpp) REVERT: B 1116 MET cc_start: 0.8791 (ttm) cc_final: 0.8521 (ttm) REVERT: B 1191 MET cc_start: 0.8078 (tpt) cc_final: 0.7844 (tpp) REVERT: B 1202 ASP cc_start: 0.8724 (m-30) cc_final: 0.8264 (t0) REVERT: C 113 MET cc_start: 0.8836 (mmm) cc_final: 0.8148 (mmm) REVERT: C 171 ASP cc_start: 0.8575 (m-30) cc_final: 0.8295 (t0) REVERT: C 544 SER cc_start: 0.8788 (m) cc_final: 0.8419 (p) REVERT: C 549 TYR cc_start: 0.5289 (m-80) cc_final: 0.5028 (m-80) REVERT: C 684 ARG cc_start: 0.8589 (mtm180) cc_final: 0.8356 (mtm-85) REVERT: C 688 GLU cc_start: 0.8460 (tt0) cc_final: 0.7960 (tm-30) REVERT: C 702 TYR cc_start: 0.8141 (t80) cc_final: 0.7863 (t80) REVERT: C 769 ASP cc_start: 0.8306 (m-30) cc_final: 0.7862 (t70) REVERT: C 1190 GLU cc_start: 0.9102 (mp0) cc_final: 0.8588 (mp0) REVERT: D 113 MET cc_start: 0.9125 (mpp) cc_final: 0.8595 (mpp) REVERT: D 456 ASP cc_start: 0.8044 (m-30) cc_final: 0.7472 (t0) REVERT: D 463 MET cc_start: 0.8213 (mmt) cc_final: 0.7276 (mtt) REVERT: D 503 MET cc_start: 0.8400 (tmm) cc_final: 0.7471 (tmm) REVERT: D 527 MET cc_start: 0.8197 (mmt) cc_final: 0.7773 (tpp) REVERT: D 693 VAL cc_start: 0.9401 (t) cc_final: 0.9104 (t) REVERT: D 1057 MET cc_start: 0.6549 (mpp) cc_final: 0.6091 (mpp) REVERT: D 1184 LEU cc_start: 0.9438 (tp) cc_final: 0.9136 (tp) REVERT: D 1202 ASP cc_start: 0.8733 (m-30) cc_final: 0.8278 (t0) outliers start: 2 outliers final: 0 residues processed: 318 average time/residue: 0.1730 time to fit residues: 92.9653 Evaluate side-chains 231 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 53 optimal weight: 5.9990 chunk 379 optimal weight: 3.9990 chunk 303 optimal weight: 0.0010 chunk 282 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 304 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 144 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.088979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.068755 restraints weight = 106526.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.069251 restraints weight = 79626.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.069622 restraints weight = 63993.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069809 restraints weight = 57374.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.069904 restraints weight = 53676.031| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.6598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31856 Z= 0.108 Angle : 0.530 7.359 43066 Z= 0.279 Chirality : 0.040 0.150 4774 Planarity : 0.003 0.049 5408 Dihedral : 4.884 74.624 4292 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.44 (0.14), residues: 3910 helix: 2.10 (0.13), residues: 1792 sheet: -0.97 (0.28), residues: 370 loop : -1.41 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 20 TYR 0.012 0.001 TYR A 405 PHE 0.026 0.001 PHE C 546 TRP 0.022 0.001 TRP A 323 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (31840) covalent geometry : angle 0.52857 / 0.28 (43034) SS BOND : bond 0.00606 / 0.38 ( 16) SS BOND : angle 1.33361 / 0.99 ( 32) hydrogen bonds : bond 0.03062 / 2.02 ( 1390) hydrogen bonds : angle 4.11844 / 2.88 ( 4020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.8585 (t0) cc_final: 0.8267 (t0) REVERT: A 113 MET cc_start: 0.8847 (mmm) cc_final: 0.8089 (mmm) REVERT: A 544 SER cc_start: 0.8871 (m) cc_final: 0.8448 (p) REVERT: A 639 LEU cc_start: 0.7731 (mp) cc_final: 0.7348 (mp) REVERT: A 728 ASP cc_start: 0.8102 (p0) cc_final: 0.7211 (m-30) REVERT: A 805 LEU cc_start: 0.9264 (tt) cc_final: 0.9043 (tt) REVERT: A 1082 PHE cc_start: 0.7424 (p90) cc_final: 0.6184 (t80) REVERT: B 113 MET cc_start: 0.9073 (mpp) cc_final: 0.8504 (mpp) REVERT: B 463 MET cc_start: 0.7856 (mpp) cc_final: 0.7595 (mmm) REVERT: B 503 MET cc_start: 0.8275 (tmm) cc_final: 0.7493 (tmm) REVERT: B 527 MET cc_start: 0.8124 (mmt) cc_final: 0.7734 (tpp) REVERT: B 670 MET cc_start: 0.8707 (tpp) cc_final: 0.8483 (mmm) REVERT: B 1022 LEU cc_start: 0.9223 (tp) cc_final: 0.9018 (tp) REVERT: B 1057 MET cc_start: 0.6450 (mpp) cc_final: 0.6165 (mpp) REVERT: B 1116 MET cc_start: 0.8833 (ttm) cc_final: 0.8569 (ttm) REVERT: B 1191 MET cc_start: 0.8148 (tpt) cc_final: 0.7908 (tpp) REVERT: B 1202 ASP cc_start: 0.8649 (m-30) cc_final: 0.8242 (t0) REVERT: C 113 MET cc_start: 0.8740 (mmm) cc_final: 0.8095 (mmm) REVERT: C 171 ASP cc_start: 0.8457 (m-30) cc_final: 0.8244 (t0) REVERT: C 544 SER cc_start: 0.8773 (m) cc_final: 0.8355 (p) REVERT: C 629 MET cc_start: 0.3606 (ppp) cc_final: 0.3370 (ppp) REVERT: C 688 GLU cc_start: 0.8388 (tt0) cc_final: 0.7901 (tm-30) REVERT: C 702 TYR cc_start: 0.8099 (t80) cc_final: 0.7791 (t80) REVERT: C 769 ASP cc_start: 0.8273 (m-30) cc_final: 0.7845 (t70) REVERT: C 1190 GLU cc_start: 0.9081 (mp0) cc_final: 0.8595 (mp0) REVERT: D 113 MET cc_start: 0.9127 (mpp) cc_final: 0.8531 (mpp) REVERT: D 456 ASP cc_start: 0.8010 (m-30) cc_final: 0.7502 (t0) REVERT: D 463 MET cc_start: 0.8101 (mmt) cc_final: 0.7114 (mtt) REVERT: D 503 MET cc_start: 0.8330 (tmm) cc_final: 0.7397 (tmm) REVERT: D 693 VAL cc_start: 0.9380 (t) cc_final: 0.9009 (t) REVERT: D 1057 MET cc_start: 0.6592 (mpp) cc_final: 0.6289 (mpp) REVERT: D 1184 LEU cc_start: 0.9437 (tp) cc_final: 0.9087 (tp) REVERT: D 1202 ASP cc_start: 0.8669 (m-30) cc_final: 0.8218 (t0) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.1666 time to fit residues: 90.2038 Evaluate side-chains 237 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 269 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 286 optimal weight: 20.0000 chunk 121 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 381 optimal weight: 0.0070 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.088400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068421 restraints weight = 106665.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068678 restraints weight = 82002.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.069007 restraints weight = 67951.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.069278 restraints weight = 59968.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.069465 restraints weight = 56204.389| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31856 Z= 0.127 Angle : 0.547 8.046 43066 Z= 0.288 Chirality : 0.040 0.157 4774 Planarity : 0.003 0.050 5408 Dihedral : 4.884 75.258 4292 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.45 (0.14), residues: 3910 helix: 2.11 (0.13), residues: 1794 sheet: -0.90 (0.28), residues: 360 loop : -1.44 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 178 TYR 0.011 0.001 TYR A 135 PHE 0.024 0.001 PHE A1072 TRP 0.020 0.001 TRP A1032 HIS 0.008 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (31840) covalent geometry : angle 0.54566 / 0.29 (43034) SS BOND : bond 0.00583 / 0.37 ( 16) SS BOND : angle 1.28774 / 0.95 ( 32) hydrogen bonds : bond 0.03221 / 2.11 ( 1390) hydrogen bonds : angle 4.17903 / 2.91 ( 4020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7820 Ramachandran restraints generated. 3910 Oldfield, 0 Emsley, 3910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.8575 (t0) cc_final: 0.8266 (t0) REVERT: A 113 MET cc_start: 0.8872 (mmm) cc_final: 0.8139 (mmm) REVERT: A 544 SER cc_start: 0.8978 (m) cc_final: 0.8556 (p) REVERT: A 728 ASP cc_start: 0.8119 (p0) cc_final: 0.7242 (m-30) REVERT: A 805 LEU cc_start: 0.9268 (tt) cc_final: 0.9058 (tt) REVERT: B 113 MET cc_start: 0.9145 (mpp) cc_final: 0.8568 (mpp) REVERT: B 463 MET cc_start: 0.7842 (mpp) cc_final: 0.7612 (mmm) REVERT: B 503 MET cc_start: 0.8317 (tmm) cc_final: 0.7557 (tmm) REVERT: B 527 MET cc_start: 0.8184 (mmt) cc_final: 0.7768 (tpp) REVERT: B 670 MET cc_start: 0.8672 (tpp) cc_final: 0.8462 (mmm) REVERT: B 1022 LEU cc_start: 0.9229 (tp) cc_final: 0.9028 (tp) REVERT: B 1116 MET cc_start: 0.8820 (ttm) cc_final: 0.8566 (ttm) REVERT: B 1202 ASP cc_start: 0.8633 (m-30) cc_final: 0.8251 (t0) REVERT: C 113 MET cc_start: 0.8762 (mmm) cc_final: 0.8127 (mmm) REVERT: C 516 SER cc_start: 0.8996 (p) cc_final: 0.7922 (p) REVERT: C 544 SER cc_start: 0.8735 (m) cc_final: 0.8339 (p) REVERT: C 688 GLU cc_start: 0.8449 (tt0) cc_final: 0.7911 (tm-30) REVERT: C 702 TYR cc_start: 0.8145 (t80) cc_final: 0.7882 (t80) REVERT: C 708 MET cc_start: 0.7811 (mmt) cc_final: 0.7563 (mmm) REVERT: C 769 ASP cc_start: 0.8255 (m-30) cc_final: 0.7854 (t70) REVERT: C 1190 GLU cc_start: 0.9117 (mp0) cc_final: 0.8638 (mp0) REVERT: D 113 MET cc_start: 0.9111 (mpp) cc_final: 0.8554 (mpp) REVERT: D 456 ASP cc_start: 0.8014 (m-30) cc_final: 0.7516 (t0) REVERT: D 463 MET cc_start: 0.8127 (mmt) cc_final: 0.7168 (mtt) REVERT: D 503 MET cc_start: 0.8385 (tmm) cc_final: 0.7455 (tmm) REVERT: D 693 VAL cc_start: 0.9397 (t) cc_final: 0.9072 (t) REVERT: D 1057 MET cc_start: 0.6714 (mpp) cc_final: 0.6476 (mpp) REVERT: D 1184 LEU cc_start: 0.9445 (tp) cc_final: 0.9085 (tp) REVERT: D 1186 PHE cc_start: 0.8718 (t80) cc_final: 0.8514 (t80) REVERT: D 1202 ASP cc_start: 0.8689 (m-30) cc_final: 0.8220 (t0) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.1639 time to fit residues: 87.3690 Evaluate side-chains 226 residues out of total 3348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 268 optimal weight: 0.1980 chunk 318 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 105 optimal weight: 0.6980 chunk 384 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 358 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 337 GLN C 147 GLN ** C 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 GLN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.069202 restraints weight = 107616.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.069699 restraints weight = 82223.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.070018 restraints weight = 66473.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.070203 restraints weight = 59840.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.070312 restraints weight = 56372.379| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 31856 Z= 0.103 Angle : 0.523 7.632 43066 Z= 0.274 Chirality : 0.040 0.150 4774 Planarity : 0.003 0.048 5408 Dihedral : 4.770 74.416 4292 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.00 % 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: 0.56 (0.14), residues: 3910 helix: 2.20 (0.13), residues: 1798 sheet: -0.91 (0.28), residues: 364 loop : -1.36 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 599 TYR 0.010 0.001 TYR D 647 PHE 0.025 0.001 PHE C 546 TRP 0.020 0.001 TRP A1032 HIS 0.007 0.001 HIS A1059 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (31840) covalent geometry : angle 0.52171 / 0.27 (43034) SS BOND : bond 0.00523 / 0.34 ( 16) SS BOND : angle 1.17908 / 0.86 ( 32) hydrogen bonds : bond 0.02905 / 1.90 ( 1390) hydrogen bonds : angle 4.03209 / 2.82 ( 4020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4341.38 seconds wall clock time: 76 minutes 14.59 seconds (4574.59 seconds total)