Starting phenix.real_space_refine on Thu May 22 02:49:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h25_0128/05_2025/6h25_0128.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h25_0128/05_2025/6h25_0128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h25_0128/05_2025/6h25_0128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h25_0128/05_2025/6h25_0128.map" model { file = "/net/cci-nas-00/data/ceres_data/6h25_0128/05_2025/6h25_0128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h25_0128/05_2025/6h25_0128.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 P 6 5.49 5 S 126 5.16 5 C 13910 2.51 5 N 3938 2.21 5 O 4158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22138 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2221 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 276} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1771 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 231} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1923 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 14, 'TRANS': 249} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 65 Chain: "D" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1570 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 202} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2144 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "F" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1752 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1527 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain breaks: 2 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2066 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 10, 'TRANS': 264} Chain breaks: 3 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "I" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 373 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 6488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6488 Classifications: {'peptide': 868} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 43, 'TRANS': 824} Chain breaks: 3 Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 405 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 15, 'TYR:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 295 Chain: "K" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 183 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 12.02, per 1000 atoms: 0.54 Number of scatterers: 22138 At special positions: 0 Unit cell: (137.7, 143.1, 152.55, 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) S 126 16.00 P 6 15.00 O 4158 8.00 N 3938 7.00 C 13910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.08 Conformation dependent library (CDL) restraints added in 3.0 seconds 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5534 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 40 sheets defined 31.8% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.636A pdb=" N LEU A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 105 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 3.627A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 243 through 277 removed outlier: 3.887A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.882A pdb=" N ALA B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 110 removed outlier: 4.500A pdb=" N SER B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 103 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.641A pdb=" N LEU B 115 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 150 Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.531A pdb=" N GLY B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 244 removed outlier: 3.853A pdb=" N ASP B 229 " --> pdb=" O HIS B 225 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 19 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.517A pdb=" N GLN C 103 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN C 117 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.511A pdb=" N ASP C 123 " --> pdb=" O GLN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.694A pdb=" N ALA C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 217 Processing helix chain 'C' and resid 244 through 273 removed outlier: 3.511A pdb=" N LEU C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 128 through 145 removed outlier: 3.767A pdb=" N CYS D 132 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 177 Processing helix chain 'D' and resid 202 through 232 removed outlier: 3.533A pdb=" N ARG D 225 " --> pdb=" O PHE D 221 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 19 Processing helix chain 'E' and resid 97 through 113 removed outlier: 3.768A pdb=" N LEU E 101 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 123 Processing helix chain 'E' and resid 147 through 162 removed outlier: 4.270A pdb=" N ALA E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 221 Processing helix chain 'E' and resid 248 through 280 removed outlier: 3.860A pdb=" N ILE E 252 " --> pdb=" O ASP E 248 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 removed outlier: 4.320A pdb=" N TYR F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 131 removed outlier: 3.937A pdb=" N GLU F 121 " --> pdb=" O CYS F 117 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 173 removed outlier: 3.808A pdb=" N ALA F 160 " --> pdb=" O SER F 156 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 233 through 266 Proline residue: F 253 - end of helix removed outlier: 3.653A pdb=" N ARG F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 146 No H-bonds generated for 'chain 'G' and resid 144 through 146' Processing helix chain 'G' and resid 203 through 211 removed outlier: 3.559A pdb=" N ILE G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 225 removed outlier: 3.682A pdb=" N GLU G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 256 Processing helix chain 'H' and resid 111 through 113 No H-bonds generated for 'chain 'H' and resid 111 through 113' Processing helix chain 'H' and resid 175 through 179 removed outlier: 4.174A pdb=" N VAL H 179 " --> pdb=" O PRO H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 247 removed outlier: 3.620A pdb=" N ASN H 239 " --> pdb=" O SER H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 264 Processing helix chain 'H' and resid 267 through 272 removed outlier: 3.715A pdb=" N ILE H 271 " --> pdb=" O ILE H 268 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU H 272 " --> pdb=" O LYS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 291 Processing helix chain 'J' and resid 69 through 76 Processing helix chain 'J' and resid 76 through 81 Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 102 through 115 removed outlier: 3.553A pdb=" N ASN J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 163 Processing helix chain 'J' and resid 177 through 188 Processing helix chain 'J' and resid 194 through 200 Processing helix chain 'J' and resid 203 through 207 removed outlier: 3.989A pdb=" N GLU J 206 " --> pdb=" O ALA J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 298 through 302 removed outlier: 3.512A pdb=" N TRP J 302 " --> pdb=" O LYS J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 437 removed outlier: 3.768A pdb=" N HIS J 437 " --> pdb=" O LEU J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 445 through 451 removed outlier: 3.529A pdb=" N SER J 450 " --> pdb=" O GLN J 446 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE J 451 " --> pdb=" O ALA J 447 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 464 removed outlier: 3.686A pdb=" N ASP J 463 " --> pdb=" O THR J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 517 through 527 Processing helix chain 'J' and resid 541 through 547 Processing helix chain 'J' and resid 589 through 599 Processing helix chain 'J' and resid 604 through 628 removed outlier: 3.589A pdb=" N ILE J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE J 625 " --> pdb=" O LYS J 621 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU J 626 " --> pdb=" O LYS J 622 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY J 628 " --> pdb=" O ARG J 624 " (cutoff:3.500A) Processing helix chain 'J' and resid 657 through 683 removed outlier: 4.225A pdb=" N SER J 661 " --> pdb=" O ARG J 657 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER J 683 " --> pdb=" O HIS J 679 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 709 removed outlier: 3.702A pdb=" N ILE J 701 " --> pdb=" O SER J 697 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU J 702 " --> pdb=" O ASN J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 717 through 727 Processing helix chain 'J' and resid 733 through 747 removed outlier: 3.954A pdb=" N ASN J 737 " --> pdb=" O PHE J 733 " (cutoff:3.500A) Processing helix chain 'J' and resid 781 through 795 removed outlier: 3.543A pdb=" N VAL J 785 " --> pdb=" O ARG J 781 " (cutoff:3.500A) Processing helix chain 'J' and resid 801 through 805 Processing helix chain 'J' and resid 806 through 842 removed outlier: 3.599A pdb=" N LEU J 810 " --> pdb=" O ASP J 806 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 822 " --> pdb=" O ASN J 818 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET J 823 " --> pdb=" O PHE J 819 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN J 825 " --> pdb=" O HIS J 821 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR J 826 " --> pdb=" O LYS J 822 " (cutoff:3.500A) Processing helix chain 'J' and resid 881 through 885 Processing helix chain 'K' and resid 82 through 96 removed outlier: 3.758A pdb=" N LYS K 86 " --> pdb=" O PRO K 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.391A pdb=" N ILE A 75 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A 134 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 77 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU A 136 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN A 79 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU A 138 " --> pdb=" O ASN A 79 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLU A 81 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.805A pdb=" N TRP A 130 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS A 122 " --> pdb=" O TRP A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 165 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 207 removed outlier: 3.704A pdb=" N TYR A 204 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU A 220 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N SER A 236 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 222 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 234 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA A 224 " --> pdb=" O CYS A 232 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR A 233 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA B 203 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN A 235 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET B 201 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER A 237 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N LEU B 199 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN B 195 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA B 188 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 199 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA B 186 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 201 " --> pdb=" O GLN B 184 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN B 184 " --> pdb=" O MET B 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 25 through 29 removed outlier: 6.264A pdb=" N LYS B 47 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 71 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE B 123 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN B 73 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL B 125 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 75 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL B 127 " --> pdb=" O GLN B 75 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N SER B 77 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLN B 129 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 35 through 39 removed outlier: 6.394A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP C 133 " --> pdb=" O CYS C 125 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS C 125 " --> pdb=" O TRP C 133 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 84 removed outlier: 7.130A pdb=" N TYR C 78 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N CYS C 137 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL C 80 " --> pdb=" O CYS C 137 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU C 139 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN C 82 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N CYS C 141 " --> pdb=" O ASN C 82 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ASP C 84 " --> pdb=" O CYS C 141 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N ASP C 143 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR C 57 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 174 through 178 removed outlier: 4.600A pdb=" N GLU C 167 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 206 through 208 removed outlier: 6.394A pdb=" N THR C 223 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU C 235 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL C 225 " --> pdb=" O CYS C 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.208A pdb=" N SER D 53 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 117 " --> pdb=" O TYR D 59 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER D 115 " --> pdb=" O PRO D 61 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR D 75 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL D 118 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU D 77 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU D 120 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 79 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL D 122 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG D 81 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N SER D 124 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.555A pdb=" N ASP D 186 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU D 192 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 66 through 67 removed outlier: 6.676A pdb=" N TRP E 133 " --> pdb=" O CYS E 125 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS E 125 " --> pdb=" O TRP E 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 78 through 85 removed outlier: 7.542A pdb=" N TYR E 78 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL E 137 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU E 80 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL E 139 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 82 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU E 141 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP E 84 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLU E 143 " --> pdb=" O ASP E 84 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP E 57 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL E 35 " --> pdb=" O ARG H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 210 through 212 removed outlier: 4.229A pdb=" N ALA E 224 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 229 " --> pdb=" O CYS E 238 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N CYS E 238 " --> pdb=" O SER E 229 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 239 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU F 225 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY E 243 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ALA F 223 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA F 214 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU F 225 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR F 212 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLY F 227 " --> pdb=" O GLY F 210 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N GLY F 210 " --> pdb=" O GLY F 227 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA F 209 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.628A pdb=" N GLY F 51 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS F 61 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F 145 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN F 143 " --> pdb=" O PRO F 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 144 " --> pdb=" O ARG F 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL F 146 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 27 through 28 removed outlier: 3.948A pdb=" N GLY G 84 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG G 85 " --> pdb=" O ASP G 103 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP G 103 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AC1, first strand: chain 'G' and resid 191 through 192 removed outlier: 7.000A pdb=" N GLU G 177 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER G 140 " --> pdb=" O MET G 178 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE G 128 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS G 124 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LYS G 130 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 165 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 199 through 201 removed outlier: 4.096A pdb=" N LEU G 227 " --> pdb=" O PHE K 77 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE K 77 " --> pdb=" O LEU G 227 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 26 through 27 Processing sheet with id=AC4, first strand: chain 'H' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'H' and resid 164 through 165 removed outlier: 7.110A pdb=" N SER H 155 " --> pdb=" O GLN H 146 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 156 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU H 109 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG H 95 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL H 91 " --> pdb=" O ARG H 95 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LYS H 97 " --> pdb=" O THR H 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AC7, first strand: chain 'I' and resid 7 through 8 removed outlier: 8.016A pdb=" N VAL I 55 " --> pdb=" O GLY I 23 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 13 through 15 removed outlier: 7.028A pdb=" N ILE I 33 " --> pdb=" O LEU I 14 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 2 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 66 through 68 removed outlier: 5.721A pdb=" N PHE J 173 " --> pdb=" O PHE J 192 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 87 through 91 removed outlier: 7.036A pdb=" N VAL J 88 " --> pdb=" O TYR J 121 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N PHE J 123 " --> pdb=" O VAL J 88 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL J 90 " --> pdb=" O PHE J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 274 through 278 removed outlier: 7.540A pdb=" N ILE J 291 " --> pdb=" O ILE J 348 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ILE J 348 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ALA J 293 " --> pdb=" O VAL J 346 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 356 through 361 removed outlier: 3.805A pdb=" N LEU J 372 " --> pdb=" O SER J 361 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG J 384 " --> pdb=" O GLY J 414 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE J 416 " --> pdb=" O ARG J 384 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASN J 413 " --> pdb=" O ASP J 403 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 417 " --> pdb=" O ILE J 399 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE J 399 " --> pdb=" O VAL J 417 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASN J 419 " --> pdb=" O ARG J 397 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ARG J 397 " --> pdb=" O ASN J 419 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG J 396 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU J 360 " --> pdb=" O ARG J 396 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 468 through 469 removed outlier: 6.464A pdb=" N GLU J 468 " --> pdb=" O VAL J 581 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN J 583 " --> pdb=" O GLU J 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS J 574 " --> pdb=" O GLU J 565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 476 through 478 removed outlier: 6.517A pdb=" N SER J 477 " --> pdb=" O LEU J 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 530 through 531 Processing sheet with id=AD8, first strand: chain 'J' and resid 638 through 640 Processing sheet with id=AD9, first strand: chain 'J' and resid 687 through 690 Processing sheet with id=AE1, first strand: chain 'J' and resid 847 through 848 removed outlier: 3.620A pdb=" N GLU J 848 " --> pdb=" O VAL J 909 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL J 909 " --> pdb=" O GLU J 848 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 851 through 855 removed outlier: 7.011A pdb=" N VAL J 861 " --> pdb=" O LEU J 853 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL J 855 " --> pdb=" O ALA J 859 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA J 859 " --> pdb=" O VAL J 855 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 886 through 887 removed outlier: 3.643A pdb=" N LEU J 894 " --> pdb=" O PHE J 901 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 912 through 914 removed outlier: 3.554A pdb=" N LYS J 922 " --> pdb=" O ASP J 914 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.18 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3750 1.31 - 1.44: 5445 1.44 - 1.57: 13124 1.57 - 1.69: 12 1.69 - 1.82: 172 Bond restraints: 22503 Sorted by residual: bond pdb=" C ILE B 25 " pdb=" O ILE B 25 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.07e-02 8.73e+03 2.36e+01 bond pdb=" N PRO J 883 " pdb=" CD PRO J 883 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO J 770 " pdb=" CD PRO J 770 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO J 802 " pdb=" CD PRO J 802 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.76e+01 bond pdb=" N PRO J 881 " pdb=" CD PRO J 881 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.72e+01 ... (remaining 22498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 29962 3.15 - 6.29: 535 6.29 - 9.44: 56 9.44 - 12.59: 13 12.59 - 15.74: 7 Bond angle restraints: 30573 Sorted by residual: angle pdb=" N GLU E 181 " pdb=" CA GLU E 181 " pdb=" C GLU E 181 " ideal model delta sigma weight residual 111.07 126.81 -15.74 1.07e+00 8.73e-01 2.16e+02 angle pdb=" CA PRO J 802 " pdb=" N PRO J 802 " pdb=" CD PRO J 802 " ideal model delta sigma weight residual 112.00 98.29 13.71 1.40e+00 5.10e-01 9.59e+01 angle pdb=" CA PRO J 883 " pdb=" N PRO J 883 " pdb=" CD PRO J 883 " ideal model delta sigma weight residual 112.00 98.31 13.69 1.40e+00 5.10e-01 9.56e+01 angle pdb=" CA PRO J 881 " pdb=" N PRO J 881 " pdb=" CD PRO J 881 " ideal model delta sigma weight residual 112.00 98.46 13.54 1.40e+00 5.10e-01 9.36e+01 angle pdb=" CA PRO J 770 " pdb=" N PRO J 770 " pdb=" CD PRO J 770 " ideal model delta sigma weight residual 112.00 98.62 13.38 1.40e+00 5.10e-01 9.14e+01 ... (remaining 30568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 13271 23.15 - 46.31: 398 46.31 - 69.46: 24 69.46 - 92.61: 9 92.61 - 115.77: 2 Dihedral angle restraints: 13704 sinusoidal: 5152 harmonic: 8552 Sorted by residual: dihedral pdb=" O4' U R 40 " pdb=" C1' U R 40 " pdb=" N1 U R 40 " pdb=" C2 U R 40 " ideal model delta sinusoidal sigma weight residual -160.00 -44.23 -115.77 1 1.50e+01 4.44e-03 6.12e+01 dihedral pdb=" CD ARG C 23 " pdb=" NE ARG C 23 " pdb=" CZ ARG C 23 " pdb=" NH1 ARG C 23 " ideal model delta sinusoidal sigma weight residual 0.00 65.72 -65.72 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CA SER J 57 " pdb=" C SER J 57 " pdb=" N SER J 58 " pdb=" CA SER J 58 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 ... (remaining 13701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 3487 0.124 - 0.249: 127 0.249 - 0.373: 10 0.373 - 0.497: 2 0.497 - 0.622: 1 Chirality restraints: 3627 Sorted by residual: chirality pdb=" CA GLU E 181 " pdb=" N GLU E 181 " pdb=" C GLU E 181 " pdb=" CB GLU E 181 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" CA ASN J 603 " pdb=" N ASN J 603 " pdb=" C ASN J 603 " pdb=" CB ASN J 603 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA LYS J 118 " pdb=" N LYS J 118 " pdb=" C LYS J 118 " pdb=" CB LYS J 118 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 3624 not shown) Planarity restraints: 3956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 23 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG C 23 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 23 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG C 23 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 23 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 880 " -0.128 5.00e-02 4.00e+02 1.80e-01 5.17e+01 pdb=" N PRO J 881 " 0.310 5.00e-02 4.00e+02 pdb=" CA PRO J 881 " -0.097 5.00e-02 4.00e+02 pdb=" CD PRO J 881 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 882 " 0.104 5.00e-02 4.00e+02 1.44e-01 3.33e+01 pdb=" N PRO J 883 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO J 883 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO J 883 " 0.074 5.00e-02 4.00e+02 ... (remaining 3953 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 5 1.86 - 2.62: 246 2.62 - 3.38: 27378 3.38 - 4.14: 48735 4.14 - 4.90: 85953 Nonbonded interactions: 162317 Sorted by model distance: nonbonded pdb=" OG SER J 599 " pdb=" OD1 ASN J 601 " model vdw 1.101 3.040 nonbonded pdb=" CE2 PHE J 840 " pdb=" CG2 ILE J 911 " model vdw 1.407 3.760 nonbonded pdb=" O ARG K 78 " pdb=" N PHE K 80 " model vdw 1.583 3.120 nonbonded pdb=" NE2 GLN J 837 " pdb=" O GLN J 921 " model vdw 1.641 3.120 nonbonded pdb=" CD LYS A 267 " pdb=" OE2 GLU A 286 " model vdw 1.808 3.440 ... (remaining 162312 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 48.190 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 22503 Z= 0.327 Angle : 1.096 15.735 30573 Z= 0.650 Chirality : 0.060 0.622 3627 Planarity : 0.011 0.448 3956 Dihedral : 11.139 115.768 8170 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.67 % Favored : 93.92 % Rotamer: Outliers : 1.51 % Allowed : 4.45 % Favored : 94.04 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.13), residues: 2929 helix: -1.64 (0.14), residues: 842 sheet: -0.65 (0.20), residues: 639 loop : -2.55 (0.13), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP J 405 HIS 0.011 0.002 HIS J 127 PHE 0.029 0.003 PHE J 451 TYR 0.024 0.003 TYR C 136 ARG 0.016 0.001 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.17185 ( 995) hydrogen bonds : angle 6.75730 ( 2871) covalent geometry : bond 0.00625 (22503) covalent geometry : angle 1.09609 (30573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 898 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8164 (tp30) cc_final: 0.7803 (tp30) REVERT: A 20 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8418 (tm-30) REVERT: A 107 GLU cc_start: 0.7995 (tt0) cc_final: 0.7773 (tt0) REVERT: A 114 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7898 (mmtp) REVERT: A 171 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7707 (mm-30) REVERT: A 181 ASP cc_start: 0.8020 (m-30) cc_final: 0.7471 (p0) REVERT: A 186 SER cc_start: 0.8351 (m) cc_final: 0.7469 (p) REVERT: A 188 HIS cc_start: 0.8357 (m-70) cc_final: 0.7946 (m-70) REVERT: A 225 MET cc_start: 0.8019 (mtp) cc_final: 0.7201 (mtp) REVERT: A 228 HIS cc_start: 0.8772 (m90) cc_final: 0.8511 (m-70) REVERT: A 229 ARG cc_start: 0.7497 (ttp80) cc_final: 0.7115 (ttm-80) REVERT: A 263 GLU cc_start: 0.8338 (tp30) cc_final: 0.8036 (tm-30) REVERT: B 15 ASP cc_start: 0.8152 (m-30) cc_final: 0.7797 (m-30) REVERT: B 21 GLU cc_start: 0.8285 (pt0) cc_final: 0.8013 (pt0) REVERT: B 36 ASP cc_start: 0.8173 (t0) cc_final: 0.7801 (t0) REVERT: B 69 ARG cc_start: 0.7875 (ptp-170) cc_final: 0.7605 (ptm160) REVERT: B 75 GLN cc_start: 0.8078 (tt0) cc_final: 0.7553 (tt0) REVERT: B 82 SER cc_start: 0.7424 (t) cc_final: 0.7152 (p) REVERT: B 118 ARG cc_start: 0.8462 (mtt180) cc_final: 0.8003 (mtp85) REVERT: B 131 ASP cc_start: 0.7774 (t0) cc_final: 0.7410 (t70) REVERT: B 155 ASP cc_start: 0.7989 (t0) cc_final: 0.7549 (t0) REVERT: B 201 MET cc_start: 0.5273 (tmm) cc_final: 0.4985 (tmm) REVERT: B 223 ASP cc_start: 0.7328 (m-30) cc_final: 0.7004 (m-30) REVERT: B 242 LEU cc_start: 0.8545 (mt) cc_final: 0.8306 (mt) REVERT: C 38 ASN cc_start: 0.7517 (m-40) cc_final: 0.7118 (m110) REVERT: C 60 CYS cc_start: 0.8452 (t) cc_final: 0.8108 (t) REVERT: C 74 PRO cc_start: 0.8003 (Cg_endo) cc_final: 0.7619 (Cg_exo) REVERT: C 75 ASP cc_start: 0.8116 (p0) cc_final: 0.6504 (t0) REVERT: C 92 ARG cc_start: 0.8870 (ptp-170) cc_final: 0.8537 (mtp-110) REVERT: C 101 GLU cc_start: 0.8197 (tp30) cc_final: 0.7798 (tp30) REVERT: C 127 SER cc_start: 0.8161 (t) cc_final: 0.7856 (p) REVERT: C 131 LEU cc_start: 0.8570 (mt) cc_final: 0.8324 (mt) REVERT: C 134 VAL cc_start: 0.7917 (t) cc_final: 0.7553 (p) REVERT: C 147 ASN cc_start: 0.8355 (t160) cc_final: 0.7592 (t0) REVERT: C 209 ASP cc_start: 0.8026 (t0) cc_final: 0.7745 (t0) REVERT: C 227 ASP cc_start: 0.7217 (t0) cc_final: 0.6178 (t70) REVERT: C 234 CYS cc_start: 0.8142 (p) cc_final: 0.7780 (t) REVERT: C 247 LYS cc_start: 0.7394 (tppt) cc_final: 0.7020 (mmtt) REVERT: C 272 SER cc_start: 0.8446 (t) cc_final: 0.8137 (m) REVERT: C 273 MET cc_start: 0.7909 (mmt) cc_final: 0.7693 (tmm) REVERT: C 274 LYS cc_start: 0.7865 (tttt) cc_final: 0.7587 (mmtt) REVERT: D 29 ARG cc_start: 0.6180 (pmt100) cc_final: 0.5934 (ptt90) REVERT: D 53 SER cc_start: 0.7808 (t) cc_final: 0.7209 (p) REVERT: D 110 LEU cc_start: 0.8502 (tp) cc_final: 0.8155 (mp) REVERT: D 149 ARG cc_start: 0.7701 (ptp-170) cc_final: 0.7500 (ptp-110) REVERT: D 168 ASP cc_start: 0.8520 (m-30) cc_final: 0.7985 (t0) REVERT: D 190 ARG cc_start: 0.8753 (mpt-90) cc_final: 0.8470 (mtt-85) REVERT: D 203 ASP cc_start: 0.7686 (p0) cc_final: 0.7360 (p0) REVERT: E 6 LEU cc_start: 0.7845 (pp) cc_final: 0.7601 (pp) REVERT: E 11 LYS cc_start: 0.7766 (mttt) cc_final: 0.7525 (mttt) REVERT: E 75 ASN cc_start: 0.8374 (p0) cc_final: 0.7525 (p0) REVERT: E 144 CYS cc_start: 0.8226 (t) cc_final: 0.7310 (m) REVERT: E 164 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7980 (mtt-85) REVERT: E 195 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7815 (pm20) REVERT: E 211 VAL cc_start: 0.8358 (t) cc_final: 0.8153 (p) REVERT: E 287 VAL cc_start: 0.8098 (t) cc_final: 0.7850 (p) REVERT: F 40 TYR cc_start: 0.7356 (t80) cc_final: 0.6820 (t80) REVERT: F 64 CYS cc_start: 0.8276 (m) cc_final: 0.7599 (m) REVERT: F 101 ARG cc_start: 0.7615 (mtt-85) cc_final: 0.7392 (mtp85) REVERT: F 108 ARG cc_start: 0.8576 (mtt90) cc_final: 0.8194 (mtt-85) REVERT: F 143 GLN cc_start: 0.7608 (pt0) cc_final: 0.7052 (pt0) REVERT: F 147 SER cc_start: 0.8000 (t) cc_final: 0.7752 (m) REVERT: F 152 GLU cc_start: 0.7610 (tt0) cc_final: 0.7171 (tt0) REVERT: F 178 ASP cc_start: 0.8459 (t0) cc_final: 0.8165 (t70) REVERT: F 194 THR cc_start: 0.8753 (m) cc_final: 0.8383 (p) REVERT: F 204 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7855 (mt-10) REVERT: F 220 ASN cc_start: 0.8244 (t0) cc_final: 0.8029 (t0) REVERT: F 234 THR cc_start: 0.8221 (m) cc_final: 0.7759 (p) REVERT: G 32 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7726 (mt-10) REVERT: G 77 ARG cc_start: 0.5223 (mtt180) cc_final: 0.4942 (mtt180) REVERT: G 156 ASN cc_start: 0.7988 (p0) cc_final: 0.7722 (t0) REVERT: G 157 VAL cc_start: 0.7817 (t) cc_final: 0.7509 (m) REVERT: G 178 MET cc_start: 0.5968 (ptm) cc_final: 0.4907 (ptt) REVERT: G 220 GLU cc_start: 0.5276 (tt0) cc_final: 0.5072 (tt0) REVERT: G 236 ARG cc_start: 0.6500 (ttm170) cc_final: 0.6204 (mtt180) REVERT: G 253 ILE cc_start: 0.7232 (mt) cc_final: 0.6934 (tp) REVERT: H 6 ARG cc_start: 0.7572 (ptp-170) cc_final: 0.7145 (ptt-90) REVERT: H 49 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7672 (pt0) REVERT: H 61 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6722 (mt-10) REVERT: H 82 ASP cc_start: 0.7536 (m-30) cc_final: 0.7312 (m-30) REVERT: H 87 ARG cc_start: 0.7135 (ttm-80) cc_final: 0.6174 (ttm-80) REVERT: H 95 ARG cc_start: 0.6552 (pmt100) cc_final: 0.6256 (ptt-90) REVERT: H 99 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6157 (tm-30) REVERT: H 112 SER cc_start: 0.8267 (m) cc_final: 0.7778 (p) REVERT: H 140 LEU cc_start: 0.7124 (mt) cc_final: 0.6810 (mt) REVERT: H 165 LYS cc_start: 0.8286 (ttpt) cc_final: 0.7925 (tttt) REVERT: H 180 LYS cc_start: 0.7665 (mtpm) cc_final: 0.6975 (mtmt) REVERT: H 246 THR cc_start: 0.7977 (m) cc_final: 0.7648 (p) REVERT: H 247 GLN cc_start: 0.7505 (mm-40) cc_final: 0.7250 (mm110) REVERT: H 249 MET cc_start: 0.8390 (ttt) cc_final: 0.8088 (ttm) REVERT: H 251 LEU cc_start: 0.8035 (tt) cc_final: 0.7774 (tt) REVERT: H 260 TYR cc_start: 0.7236 (t80) cc_final: 0.6963 (t80) REVERT: I 16 ASN cc_start: 0.6364 (m-40) cc_final: 0.5452 (p0) REVERT: J 22 GLU cc_start: 0.8028 (pt0) cc_final: 0.7523 (pt0) REVERT: J 69 ASP cc_start: 0.7381 (t0) cc_final: 0.6865 (t70) REVERT: J 82 ASP cc_start: 0.6554 (t70) cc_final: 0.6272 (t70) REVERT: J 102 SER cc_start: 0.6440 (t) cc_final: 0.6105 (p) REVERT: J 122 THR cc_start: 0.8274 (m) cc_final: 0.8033 (t) REVERT: J 169 LEU cc_start: 0.8391 (mt) cc_final: 0.8183 (mp) REVERT: J 170 GLN cc_start: 0.7537 (mm-40) cc_final: 0.6970 (tt0) REVERT: J 175 THR cc_start: 0.8717 (t) cc_final: 0.8508 (p) REVERT: J 259 LEU cc_start: 0.8307 (mt) cc_final: 0.8088 (mm) REVERT: J 285 ARG cc_start: 0.4733 (ptp-170) cc_final: 0.4527 (ptp90) REVERT: J 357 CYS cc_start: 0.8010 (m) cc_final: 0.7771 (m) REVERT: J 367 GLU cc_start: 0.8440 (mp0) cc_final: 0.8151 (mp0) REVERT: J 379 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7199 (mtm-85) REVERT: J 474 CYS cc_start: 0.4611 (p) cc_final: 0.4284 (m) REVERT: J 522 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7786 (tt0) REVERT: J 569 ASN cc_start: 0.8875 (m-40) cc_final: 0.8642 (t0) REVERT: J 588 LEU cc_start: 0.6212 (mt) cc_final: 0.5868 (mt) REVERT: J 602 MET cc_start: 0.3969 (OUTLIER) cc_final: 0.3426 (mtt) REVERT: J 624 ARG cc_start: 0.8775 (ttp-170) cc_final: 0.8367 (tpm170) REVERT: J 665 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5768 (mm-30) REVERT: J 667 MET cc_start: 0.8317 (mmp) cc_final: 0.7909 (mmm) REVERT: J 671 ASN cc_start: 0.7827 (m-40) cc_final: 0.7580 (m110) REVERT: J 676 LYS cc_start: 0.7368 (mttt) cc_final: 0.7094 (tttp) REVERT: J 712 GLU cc_start: 0.4598 (OUTLIER) cc_final: 0.4088 (pp20) REVERT: J 735 TYR cc_start: 0.7418 (t80) cc_final: 0.6910 (t80) REVERT: J 748 MET cc_start: 0.6172 (mmp) cc_final: 0.5941 (mmm) REVERT: J 841 LYS cc_start: 0.5403 (OUTLIER) cc_final: 0.4922 (tppp) REVERT: J 925 MET cc_start: 0.6986 (mmt) cc_final: 0.6716 (mmt) outliers start: 34 outliers final: 12 residues processed: 925 average time/residue: 0.3754 time to fit residues: 507.1637 Evaluate side-chains 631 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 616 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 601 ASN Chi-restraints excluded: chain J residue 602 MET Chi-restraints excluded: chain J residue 687 LEU Chi-restraints excluded: chain J residue 712 GLU Chi-restraints excluded: chain J residue 750 GLN Chi-restraints excluded: chain J residue 800 THR Chi-restraints excluded: chain J residue 838 LEU Chi-restraints excluded: chain J residue 839 PHE Chi-restraints excluded: chain J residue 841 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 9.9990 chunk 221 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 118 optimal weight: 0.0170 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 265 optimal weight: 5.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 159 HIS A 189 HIS B 102 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN C 192 HIS D 30 HIS D 121 GLN D 229 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN E 285 GLN F 143 GLN F 257 GLN H 185 HIS J 92 GLN J 127 HIS J 146 ASN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 HIS J 288 HIS J 737 ASN J 750 GLN J 763 HIS J 825 GLN J 835 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.179417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.149860 restraints weight = 30932.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.151289 restraints weight = 19679.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.151793 restraints weight = 14758.778| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22503 Z= 0.142 Angle : 0.649 8.888 30573 Z= 0.336 Chirality : 0.044 0.276 3627 Planarity : 0.005 0.070 3956 Dihedral : 7.792 104.859 3314 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.61 % Favored : 95.32 % Rotamer: Outliers : 4.27 % Allowed : 13.61 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 2929 helix: 0.40 (0.17), residues: 849 sheet: -0.37 (0.19), residues: 677 loop : -2.04 (0.15), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 155 HIS 0.006 0.001 HIS J 127 PHE 0.024 0.002 PHE D 221 TYR 0.018 0.001 TYR E 110 ARG 0.006 0.001 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 995) hydrogen bonds : angle 4.91189 ( 2871) covalent geometry : bond 0.00309 (22503) covalent geometry : angle 0.64890 (30573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 668 time to evaluate : 2.657 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9164 (tt) REVERT: A 99 LEU cc_start: 0.9370 (tt) cc_final: 0.9115 (tt) REVERT: A 103 ASN cc_start: 0.9091 (t0) cc_final: 0.8579 (t0) REVERT: A 190 MET cc_start: 0.8418 (mtm) cc_final: 0.7937 (mtt) REVERT: A 217 MET cc_start: 0.9088 (ptt) cc_final: 0.8825 (ptt) REVERT: A 225 MET cc_start: 0.8457 (mtp) cc_final: 0.8125 (mtp) REVERT: A 281 LYS cc_start: 0.7395 (mmmt) cc_final: 0.7106 (mptt) REVERT: B 25 ILE cc_start: 0.8835 (pt) cc_final: 0.8631 (pt) REVERT: B 156 PHE cc_start: 0.8563 (t80) cc_final: 0.8314 (t80) REVERT: B 198 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8697 (tp) REVERT: C 38 ASN cc_start: 0.8048 (m-40) cc_final: 0.7746 (m110) REVERT: C 60 CYS cc_start: 0.8011 (t) cc_final: 0.7742 (t) REVERT: C 75 ASP cc_start: 0.7685 (p0) cc_final: 0.7354 (t0) REVERT: C 83 VAL cc_start: 0.9225 (t) cc_final: 0.8955 (p) REVERT: C 115 ASN cc_start: 0.8528 (m-40) cc_final: 0.8267 (m-40) REVERT: C 162 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7835 (t0) REVERT: C 227 ASP cc_start: 0.8174 (t0) cc_final: 0.7896 (t0) REVERT: C 236 HIS cc_start: 0.8123 (t70) cc_final: 0.7872 (t70) REVERT: C 267 ASP cc_start: 0.7859 (m-30) cc_final: 0.7653 (m-30) REVERT: D 29 ARG cc_start: 0.7037 (OUTLIER) cc_final: 0.6216 (ptt90) REVERT: D 96 ARG cc_start: 0.8972 (ttt180) cc_final: 0.8691 (ttt-90) REVERT: D 110 LEU cc_start: 0.8973 (tp) cc_final: 0.8687 (mp) REVERT: E 32 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: F 143 GLN cc_start: 0.8344 (pt0) cc_final: 0.7856 (pt0) REVERT: F 176 MET cc_start: 0.8577 (mtp) cc_final: 0.8321 (mtt) REVERT: F 194 THR cc_start: 0.8903 (m) cc_final: 0.8663 (p) REVERT: F 206 ARG cc_start: 0.8107 (mmt-90) cc_final: 0.7404 (mpt-90) REVERT: F 239 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6413 (tp30) REVERT: G 113 LYS cc_start: 0.6406 (tttp) cc_final: 0.6168 (tttp) REVERT: G 157 VAL cc_start: 0.8298 (t) cc_final: 0.8061 (m) REVERT: G 253 ILE cc_start: 0.8327 (mt) cc_final: 0.7853 (tp) REVERT: H 87 ARG cc_start: 0.8722 (ttm-80) cc_final: 0.8329 (ttm-80) REVERT: H 99 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7379 (tp30) REVERT: H 247 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7739 (mm-40) REVERT: I 16 ASN cc_start: 0.8313 (m-40) cc_final: 0.6732 (p0) REVERT: J 110 ARG cc_start: 0.8762 (mmm-85) cc_final: 0.8184 (tpp80) REVERT: J 285 ARG cc_start: 0.6998 (ptp-170) cc_final: 0.6120 (ptt180) REVERT: J 508 ASP cc_start: 0.8518 (t0) cc_final: 0.8240 (t0) REVERT: J 521 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7413 (mt0) REVERT: J 665 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6214 (mm-30) REVERT: J 671 ASN cc_start: 0.7835 (m-40) cc_final: 0.7237 (m-40) REVERT: J 676 LYS cc_start: 0.7621 (mttt) cc_final: 0.7417 (tttp) REVERT: J 682 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6630 (m-80) REVERT: J 776 THR cc_start: 0.8947 (p) cc_final: 0.8709 (t) REVERT: J 841 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6642 (tppp) REVERT: J 922 LYS cc_start: 0.7309 (ttpt) cc_final: 0.6996 (ptpp) outliers start: 96 outliers final: 47 residues processed: 723 average time/residue: 0.3266 time to fit residues: 360.8583 Evaluate side-chains 595 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 541 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 250 ASP Chi-restraints excluded: chain D residue 29 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 510 SER Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 841 LYS Chi-restraints excluded: chain J residue 863 LEU Chi-restraints excluded: chain J residue 918 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 186 optimal weight: 0.9990 chunk 288 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 77 optimal weight: 0.0770 chunk 291 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 141 HIS B 102 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN D 30 HIS D 173 GLN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS H 239 ASN ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 415 HIS J 763 HIS J 828 GLN J 920 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.173257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.143037 restraints weight = 31017.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.143642 restraints weight = 19914.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.144620 restraints weight = 15332.447| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22503 Z= 0.154 Angle : 0.628 9.807 30573 Z= 0.321 Chirality : 0.044 0.219 3627 Planarity : 0.004 0.056 3956 Dihedral : 7.186 100.176 3293 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 4.58 % Allowed : 18.02 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 2929 helix: 1.20 (0.17), residues: 851 sheet: -0.29 (0.19), residues: 667 loop : -1.77 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 302 HIS 0.012 0.001 HIS H 157 PHE 0.018 0.002 PHE C 154 TYR 0.014 0.001 TYR H 206 ARG 0.005 0.000 ARG J 924 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 995) hydrogen bonds : angle 4.59185 ( 2871) covalent geometry : bond 0.00356 (22503) covalent geometry : angle 0.62810 (30573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 571 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8921 (mttt) cc_final: 0.8439 (pttm) REVERT: A 98 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9130 (tt) REVERT: A 171 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7716 (mt-10) REVERT: A 190 MET cc_start: 0.8615 (mtm) cc_final: 0.8106 (mtt) REVERT: A 217 MET cc_start: 0.9115 (ptt) cc_final: 0.8667 (ptt) REVERT: A 242 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9022 (pp) REVERT: A 281 LYS cc_start: 0.7487 (mmmt) cc_final: 0.7126 (mptt) REVERT: C 60 CYS cc_start: 0.8013 (t) cc_final: 0.7742 (t) REVERT: C 75 ASP cc_start: 0.7744 (p0) cc_final: 0.7330 (t0) REVERT: C 83 VAL cc_start: 0.9288 (t) cc_final: 0.9002 (p) REVERT: C 115 ASN cc_start: 0.8582 (m-40) cc_final: 0.8296 (m-40) REVERT: C 189 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8664 (tp) REVERT: C 267 ASP cc_start: 0.7786 (m-30) cc_final: 0.7519 (m-30) REVERT: D 110 LEU cc_start: 0.8977 (tp) cc_final: 0.8661 (mp) REVERT: E 32 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: E 182 LEU cc_start: 0.9199 (tm) cc_final: 0.8991 (tm) REVERT: F 143 GLN cc_start: 0.8464 (pt0) cc_final: 0.7836 (pt0) REVERT: F 176 MET cc_start: 0.8717 (mtp) cc_final: 0.8363 (mtt) REVERT: F 186 SER cc_start: 0.9239 (t) cc_final: 0.8982 (m) REVERT: F 194 THR cc_start: 0.8824 (m) cc_final: 0.8581 (p) REVERT: G 113 LYS cc_start: 0.6650 (tttp) cc_final: 0.6331 (tttp) REVERT: G 168 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8493 (p) REVERT: G 253 ILE cc_start: 0.8347 (mt) cc_final: 0.7894 (tp) REVERT: H 87 ARG cc_start: 0.8873 (ttm-80) cc_final: 0.8563 (ttm-80) REVERT: H 99 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7375 (tp30) REVERT: H 131 MET cc_start: 0.7100 (ttp) cc_final: 0.6858 (ttp) REVERT: I 16 ASN cc_start: 0.8357 (m-40) cc_final: 0.6763 (p0) REVERT: J 110 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8565 (tpp80) REVERT: J 259 LEU cc_start: 0.9201 (mm) cc_final: 0.8980 (mp) REVERT: J 379 ARG cc_start: 0.8811 (mtm-85) cc_final: 0.8523 (mtm-85) REVERT: J 521 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7538 (mt0) REVERT: J 545 SER cc_start: 0.9110 (t) cc_final: 0.8824 (p) REVERT: J 676 LYS cc_start: 0.7852 (mttt) cc_final: 0.7593 (tttp) REVERT: J 682 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: J 735 TYR cc_start: 0.7428 (t80) cc_final: 0.7115 (t80) REVERT: J 748 MET cc_start: 0.6743 (mmp) cc_final: 0.6437 (mmm) REVERT: J 826 TYR cc_start: 0.8427 (m-80) cc_final: 0.8121 (m-80) REVERT: J 841 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6708 (tppp) outliers start: 103 outliers final: 69 residues processed: 634 average time/residue: 0.3477 time to fit residues: 341.5222 Evaluate side-chains 608 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 532 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 218 GLN Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 242 ILE Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 435 LEU Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 841 LYS Chi-restraints excluded: chain J residue 918 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 207 optimal weight: 7.9990 chunk 216 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 171 optimal weight: 0.0570 chunk 13 optimal weight: 0.6980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 34 ASN C 162 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.176444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.147189 restraints weight = 31325.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.147008 restraints weight = 20108.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.148877 restraints weight = 15808.687| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22503 Z= 0.124 Angle : 0.595 9.221 30573 Z= 0.300 Chirality : 0.043 0.163 3627 Planarity : 0.004 0.056 3956 Dihedral : 6.823 96.305 3293 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.88 % Favored : 95.08 % Rotamer: Outliers : 5.12 % Allowed : 18.68 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2929 helix: 1.61 (0.18), residues: 850 sheet: -0.03 (0.20), residues: 629 loop : -1.57 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 302 HIS 0.009 0.001 HIS H 157 PHE 0.019 0.001 PHE D 221 TYR 0.014 0.001 TYR H 252 ARG 0.006 0.000 ARG J 924 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 995) hydrogen bonds : angle 4.35375 ( 2871) covalent geometry : bond 0.00278 (22503) covalent geometry : angle 0.59548 (30573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 575 time to evaluate : 2.431 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8872 (mttt) cc_final: 0.8465 (pttm) REVERT: A 98 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9120 (tt) REVERT: A 103 ASN cc_start: 0.9094 (t0) cc_final: 0.8684 (t0) REVERT: A 108 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8834 (ttm170) REVERT: A 142 ASP cc_start: 0.8640 (t70) cc_final: 0.8247 (t70) REVERT: A 171 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7596 (tt0) REVERT: A 190 MET cc_start: 0.8591 (mtm) cc_final: 0.8081 (mtt) REVERT: A 217 MET cc_start: 0.9065 (ptt) cc_final: 0.8583 (ptt) REVERT: A 281 LYS cc_start: 0.7658 (mmmt) cc_final: 0.7223 (mptt) REVERT: B 26 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7913 (pt0) REVERT: B 155 ASP cc_start: 0.8453 (t0) cc_final: 0.8162 (t0) REVERT: C 60 CYS cc_start: 0.7987 (t) cc_final: 0.7714 (t) REVERT: C 75 ASP cc_start: 0.7814 (p0) cc_final: 0.7462 (t0) REVERT: C 83 VAL cc_start: 0.9269 (t) cc_final: 0.8989 (p) REVERT: C 115 ASN cc_start: 0.8642 (m-40) cc_final: 0.8321 (m-40) REVERT: E 32 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: E 116 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8529 (tmmt) REVERT: E 143 GLU cc_start: 0.7110 (tp30) cc_final: 0.6826 (tp30) REVERT: E 164 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.7511 (mtm-85) REVERT: E 182 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8768 (tm) REVERT: F 176 MET cc_start: 0.8679 (mtp) cc_final: 0.8421 (mtt) REVERT: F 178 ASP cc_start: 0.8429 (t0) cc_final: 0.8218 (t0) REVERT: F 194 THR cc_start: 0.8795 (m) cc_final: 0.8528 (p) REVERT: F 250 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7500 (ptp90) REVERT: G 113 LYS cc_start: 0.6737 (tttp) cc_final: 0.6361 (tttp) REVERT: G 253 ILE cc_start: 0.8368 (mt) cc_final: 0.7877 (tp) REVERT: H 47 MET cc_start: 0.8691 (mmm) cc_final: 0.8237 (mmm) REVERT: H 87 ARG cc_start: 0.8891 (ttm-80) cc_final: 0.8570 (ttm-80) REVERT: H 99 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7300 (tp30) REVERT: H 155 SER cc_start: 0.9051 (t) cc_final: 0.8841 (p) REVERT: I 16 ASN cc_start: 0.8400 (m-40) cc_final: 0.6930 (p0) REVERT: J 110 ARG cc_start: 0.8855 (mmm-85) cc_final: 0.8498 (tpp80) REVERT: J 245 THR cc_start: 0.7607 (p) cc_final: 0.7153 (t) REVERT: J 259 LEU cc_start: 0.9153 (mm) cc_final: 0.8900 (mp) REVERT: J 350 LYS cc_start: 0.8310 (tttm) cc_final: 0.8110 (tptp) REVERT: J 433 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8487 (tp) REVERT: J 545 SER cc_start: 0.8987 (t) cc_final: 0.8716 (p) REVERT: J 623 ARG cc_start: 0.7326 (mtp180) cc_final: 0.6905 (mtp180) REVERT: J 667 MET cc_start: 0.9306 (mmp) cc_final: 0.8901 (mmt) REVERT: J 671 ASN cc_start: 0.7773 (m-40) cc_final: 0.7293 (m-40) REVERT: J 682 PHE cc_start: 0.6824 (OUTLIER) cc_final: 0.5905 (m-80) REVERT: J 748 MET cc_start: 0.6687 (mmp) cc_final: 0.6439 (mmm) REVERT: J 826 TYR cc_start: 0.8384 (m-80) cc_final: 0.8132 (m-80) outliers start: 115 outliers final: 71 residues processed: 640 average time/residue: 0.3295 time to fit residues: 327.9276 Evaluate side-chains 607 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 527 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 108 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 204 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN H 157 HIS H 185 HIS ** J 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 231 HIS J 788 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.169761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.139008 restraints weight = 31292.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140525 restraints weight = 19638.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.141934 restraints weight = 13324.102| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22503 Z= 0.129 Angle : 0.601 13.657 30573 Z= 0.299 Chirality : 0.043 0.164 3627 Planarity : 0.004 0.053 3956 Dihedral : 6.594 93.787 3289 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 5.34 % Allowed : 19.44 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.15), residues: 2929 helix: 1.80 (0.18), residues: 854 sheet: 0.03 (0.20), residues: 636 loop : -1.47 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 302 HIS 0.007 0.001 HIS H 157 PHE 0.029 0.001 PHE E 289 TYR 0.015 0.001 TYR H 252 ARG 0.006 0.000 ARG H 6 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 995) hydrogen bonds : angle 4.29564 ( 2871) covalent geometry : bond 0.00298 (22503) covalent geometry : angle 0.60135 (30573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5858 Ramachandran restraints generated. 2929 Oldfield, 0 Emsley, 2929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 558 time to evaluate : 2.389 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "LEU E 280 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7569 (tm-30) REVERT: A 21 LYS cc_start: 0.8876 (mttt) cc_final: 0.8494 (pttm) REVERT: A 98 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9128 (tt) REVERT: A 103 ASN cc_start: 0.9058 (t0) cc_final: 0.8703 (t0) REVERT: A 142 ASP cc_start: 0.8794 (t70) cc_final: 0.8354 (t70) REVERT: A 171 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7497 (tt0) REVERT: A 190 MET cc_start: 0.8663 (mtm) cc_final: 0.8233 (mtt) REVERT: A 272 ASP cc_start: 0.7892 (t70) cc_final: 0.7657 (t0) REVERT: A 281 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7181 (mptt) REVERT: B 26 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7996 (pt0) REVERT: B 155 ASP cc_start: 0.8624 (t0) cc_final: 0.8316 (t0) REVERT: C 60 CYS cc_start: 0.8029 (t) cc_final: 0.7768 (t) REVERT: C 75 ASP cc_start: 0.7913 (p0) cc_final: 0.7496 (t0) REVERT: C 83 VAL cc_start: 0.9289 (t) cc_final: 0.8991 (p) REVERT: C 115 ASN cc_start: 0.8634 (m-40) cc_final: 0.8315 (m-40) REVERT: C 227 ASP cc_start: 0.8463 (m-30) cc_final: 0.8132 (m-30) REVERT: D 193 LEU cc_start: 0.9291 (mt) cc_final: 0.9084 (mt) REVERT: E 32 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: E 143 GLU cc_start: 0.7079 (tp30) cc_final: 0.6815 (tp30) REVERT: E 182 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8763 (tm) REVERT: F 175 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7340 (mt-10) REVERT: F 176 MET cc_start: 0.8498 (mtp) cc_final: 0.8245 (mtt) REVERT: F 194 THR cc_start: 0.8796 (m) cc_final: 0.8483 (p) REVERT: F 250 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7452 (ptp90) REVERT: G 113 LYS cc_start: 0.6903 (tttp) cc_final: 0.6616 (tttp) REVERT: G 236 ARG cc_start: 0.8613 (ttm170) cc_final: 0.7591 (mtt180) REVERT: G 253 ILE cc_start: 0.8374 (mt) cc_final: 0.7740 (tp) REVERT: H 87 ARG cc_start: 0.8913 (ttm-80) cc_final: 0.8512 (ttm-80) REVERT: H 99 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7332 (tp30) REVERT: H 284 THR cc_start: 0.8609 (t) cc_final: 0.8384 (m) REVERT: I 16 ASN cc_start: 0.8437 (m-40) cc_final: 0.6973 (p0) REVERT: J 110 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.8477 (tpp80) REVERT: J 245 THR cc_start: 0.7708 (p) cc_final: 0.7246 (t) REVERT: J 259 LEU cc_start: 0.9141 (mm) cc_final: 0.8889 (mp) REVERT: J 350 LYS cc_start: 0.8363 (tttm) cc_final: 0.8163 (tptp) REVERT: J 433 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8545 (tp) REVERT: J 491 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.5739 (p-80) REVERT: J 543 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7779 (tt) REVERT: J 623 ARG cc_start: 0.7313 (mtp180) cc_final: 0.6880 (mtp180) REVERT: J 671 ASN cc_start: 0.7870 (m-40) cc_final: 0.7405 (m-40) REVERT: J 682 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: J 748 MET cc_start: 0.6830 (mmp) cc_final: 0.6560 (mmm) REVERT: J 826 TYR cc_start: 0.8445 (m-80) cc_final: 0.8234 (m-80) REVERT: J 919 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8031 (mm-40) outliers start: 120 outliers final: 89 residues processed: 625 average time/residue: 0.3162 time to fit residues: 305.9595 Evaluate side-chains 621 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 523 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 116 LYS Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 226 LEU Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 178 MET Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 GLU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 227 SER Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 280 ILE Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 122 THR Chi-restraints excluded: chain J residue 155 TRP Chi-restraints excluded: chain J residue 156 TYR Chi-restraints excluded: chain J residue 250 THR Chi-restraints excluded: chain J residue 254 SER Chi-restraints excluded: chain J residue 287 VAL Chi-restraints excluded: chain J residue 290 ASP Chi-restraints excluded: chain J residue 295 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 491 HIS Chi-restraints excluded: chain J residue 528 THR Chi-restraints excluded: chain J residue 543 LEU Chi-restraints excluded: chain J residue 625 ILE Chi-restraints excluded: chain J residue 682 PHE Chi-restraints excluded: chain J residue 763 HIS Chi-restraints excluded: chain J residue 773 THR Chi-restraints excluded: chain J residue 799 CYS Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 913 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.4672 > 50: distance: 29 - 150: 28.351 distance: 42 - 130: 32.061 distance: 45 - 127: 22.675 distance: 81 - 87: 26.129 distance: 87 - 88: 21.351 distance: 88 - 89: 18.136 distance: 88 - 91: 20.314 distance: 89 - 90: 27.797 distance: 89 - 94: 38.238 distance: 91 - 92: 19.791 distance: 91 - 93: 19.021 distance: 94 - 95: 13.580 distance: 95 - 96: 27.909 distance: 95 - 98: 13.307 distance: 96 - 97: 20.828 distance: 96 - 103: 15.155 distance: 98 - 99: 24.007 distance: 100 - 101: 8.449 distance: 100 - 102: 8.547 distance: 103 - 104: 22.571 distance: 104 - 105: 23.464 distance: 104 - 107: 16.219 distance: 105 - 106: 15.017 distance: 105 - 110: 19.887 distance: 107 - 108: 26.823 distance: 110 - 111: 17.428 distance: 111 - 112: 14.839 distance: 112 - 113: 8.695 distance: 112 - 114: 48.724 distance: 114 - 115: 14.838 distance: 115 - 116: 13.060 distance: 115 - 118: 41.276 distance: 116 - 117: 36.191 distance: 116 - 119: 10.306 distance: 119 - 120: 40.298 distance: 120 - 121: 29.838 distance: 120 - 123: 16.435 distance: 121 - 127: 15.501 distance: 123 - 124: 9.357 distance: 124 - 125: 11.422 distance: 124 - 126: 27.927 distance: 127 - 128: 17.551 distance: 128 - 129: 34.478 distance: 128 - 131: 19.388 distance: 129 - 130: 44.266 distance: 129 - 135: 30.251 distance: 131 - 132: 12.388 distance: 131 - 133: 13.554 distance: 132 - 134: 4.785 distance: 135 - 136: 30.332 distance: 135 - 204: 9.200 distance: 136 - 137: 30.395 distance: 136 - 139: 25.323 distance: 137 - 138: 29.763 distance: 137 - 147: 32.076 distance: 138 - 201: 28.190 distance: 139 - 140: 27.171 distance: 140 - 141: 9.640 distance: 140 - 142: 13.289 distance: 141 - 143: 10.751 distance: 142 - 144: 11.413 distance: 143 - 145: 7.258 distance: 144 - 145: 7.532 distance: 145 - 146: 12.492 distance: 147 - 148: 15.633 distance: 148 - 149: 15.635 distance: 149 - 150: 33.981 distance: 149 - 151: 32.239 distance: 151 - 152: 22.284 distance: 151 - 184: 28.765 distance: 152 - 155: 31.673 distance: 153 - 154: 36.468 distance: 153 - 160: 12.518 distance: 154 - 181: 35.704 distance: 155 - 156: 30.106 distance: 156 - 157: 16.861 distance: 157 - 158: 3.850 distance: 157 - 159: 12.240