Starting phenix.real_space_refine on Sat Jan 25 04:47:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9c_39859/01_2025/8z9c_39859_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9c_39859/01_2025/8z9c_39859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9c_39859/01_2025/8z9c_39859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9c_39859/01_2025/8z9c_39859.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9c_39859/01_2025/8z9c_39859_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9c_39859/01_2025/8z9c_39859_neut.cif" } resolution = 3.01 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= 0.002 sd= 0.049 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: 6 Type Number sf(0) Gaussians Zn 9 6.06 5 P 89 5.49 5 S 95 5.16 5 C 14301 2.51 5 N 3995 2.21 5 O 4693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23182 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1154 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 153} Chain breaks: 3 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1535 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1547 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 5, 'TRANS': 193} Chain: "D" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1543 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1541 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 193} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1465 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 188} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1658 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "H" Number of atoms: 4486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4486 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 5 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "I" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1330 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1532 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 192} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2182 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 8 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "L" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1320 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 1003 Classifications: {'RNA': 48} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 24, 'rna3p': 23} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {' G%rna2p_pur:plan': 1, ' G%rna2p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 877 Classifications: {'RNA': 41} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 15} Link IDs: {'rna2p': 8, 'rna3p': 32} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 375 SG CYS A 71 33.614 55.852 184.378 1.00125.23 S ATOM 444 SG CYS A 81 30.838 55.036 181.981 1.00122.46 S ATOM 465 SG CYS A 84 30.069 57.529 184.598 1.00119.18 S ATOM 485 SG CYS A 87 32.391 58.529 181.904 1.00113.92 S ATOM 1704 SG CYS B 71 24.938 78.749 160.321 1.00 76.24 S ATOM 1778 SG CYS B 81 22.333 80.254 157.702 1.00 64.00 S ATOM 1819 SG CYS B 87 26.042 80.981 158.998 1.00 60.98 S ATOM 3241 SG CYS C 71 38.215 97.557 135.445 1.00 67.44 S ATOM 3315 SG CYS C 81 38.198 100.653 132.790 1.00 64.87 S ATOM 3336 SG CYS C 84 39.666 100.838 135.363 1.00 65.58 S ATOM 3356 SG CYS C 87 41.310 98.088 133.210 1.00 51.36 S ATOM 4788 SG CYS D 71 75.833 76.073 87.589 1.00 66.71 S ATOM 4862 SG CYS D 81 78.364 75.235 84.999 1.00 69.68 S ATOM 4883 SG CYS D 84 77.834 72.788 87.737 1.00 64.63 S ATOM 4903 SG CYS D 87 75.110 73.073 85.318 1.00 53.51 S ATOM 6331 SG CYS E 71 66.447 51.959 65.256 1.00 80.64 S ATOM 6405 SG CYS E 81 67.038 49.101 62.882 1.00 98.21 S ATOM 6426 SG CYS E 84 67.562 48.223 64.882 1.00 96.79 S ATOM 6446 SG CYS E 87 64.528 50.672 63.062 1.00 64.49 S ATOM 7861 SG CYS F 71 42.366 43.340 42.195 1.00108.96 S ATOM 7934 SG CYS F 84 39.271 43.962 44.503 1.00104.95 S ATOM 7954 SG CYS F 87 40.612 45.934 41.547 1.00 97.31 S ATOM 9309 SG CYS G 70 37.798 92.104 32.715 1.00124.51 S ATOM 9421 SG CYS G 85 40.802 92.369 31.454 1.00 30.00 S ATOM 9440 SG CYS G 88 40.679 95.321 34.203 1.00121.90 S ATOM 16800 SG CYS J 71 62.418 96.536 110.973 1.00 51.29 S ATOM 16874 SG CYS J 81 64.881 97.976 108.436 1.00 63.36 S ATOM 16895 SG CYS J 84 66.212 95.782 111.269 1.00 69.14 S ATOM 16915 SG CYS J 87 64.111 94.213 108.655 1.00 59.64 S Time building chain proxies: 13.65, per 1000 atoms: 0.59 Number of scatterers: 23182 At special positions: 0 Unit cell: (93.1, 122.55, 217.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 9 29.99 S 95 16.00 P 89 15.00 O 4693 8.00 N 3995 7.00 C 14301 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: 6.00 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 84 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 81 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 71 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 71 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 84 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 71 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 87 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 84 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 71 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 87 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 81 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 71 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 87 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 81 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 84 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 71 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 87 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 84 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 85 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 70 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 88 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 64 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 148 " pdb="ZN ZN H 701 " - pdb=" NE2 HIS H 62 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 87 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 84 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 71 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 81 " Number of angles added : 30 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 33 sheets defined 34.2% alpha, 18.9% beta 23 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 7.72 Creating SS restraints... Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 155 through 171 removed outlier: 4.743A pdb=" N SER A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 31 Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.790A pdb=" N GLU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.638A pdb=" N GLY B 180 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 31 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.700A pdb=" N SER C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 166 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 30 Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.580A pdb=" N GLY D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.580A pdb=" N PHE D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 30 Processing helix chain 'E' and resid 51 through 67 removed outlier: 3.522A pdb=" N GLY E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 90 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 156 through 172 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.544A pdb=" N ARG E 197 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE E 198 " --> pdb=" O THR E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 51 through 67 Processing helix chain 'F' and resid 84 through 90 removed outlier: 3.656A pdb=" N LEU F 89 " --> pdb=" O VAL F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 171 removed outlier: 4.574A pdb=" N SER F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'G' and resid 47 through 53 removed outlier: 4.084A pdb=" N ASP G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 127 through 142 Processing helix chain 'H' and resid 42 through 53 removed outlier: 3.959A pdb=" N GLY H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 86 through 107 removed outlier: 3.752A pdb=" N LEU H 95 " --> pdb=" O GLU H 91 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASN H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 124 Processing helix chain 'H' and resid 207 through 221 removed outlier: 3.972A pdb=" N LEU H 211 " --> pdb=" O ASP H 207 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU H 212 " --> pdb=" O ARG H 208 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU H 220 " --> pdb=" O LYS H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 245 removed outlier: 3.633A pdb=" N TYR H 240 " --> pdb=" O GLN H 236 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR H 245 " --> pdb=" O THR H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 295 through 304 Processing helix chain 'H' and resid 322 through 333 removed outlier: 4.181A pdb=" N HIS H 326 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU H 328 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN H 329 " --> pdb=" O ASN H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 355 removed outlier: 3.566A pdb=" N LYS H 352 " --> pdb=" O THR H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 385 Processing helix chain 'H' and resid 399 through 413 Processing helix chain 'H' and resid 471 through 481 Processing helix chain 'H' and resid 509 through 523 Processing helix chain 'H' and resid 527 through 541 Processing helix chain 'H' and resid 541 through 554 Processing helix chain 'H' and resid 572 through 593 removed outlier: 3.860A pdb=" N LYS H 592 " --> pdb=" O LEU H 588 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR H 593 " --> pdb=" O SER H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 594 through 602 Processing helix chain 'I' and resid 470 through 488 removed outlier: 3.893A pdb=" N PHE I 474 " --> pdb=" O ASP I 470 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET I 476 " --> pdb=" O ASN I 472 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN I 488 " --> pdb=" O LYS I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 523 Processing helix chain 'I' and resid 527 through 541 Processing helix chain 'I' and resid 541 through 554 Processing helix chain 'I' and resid 572 through 592 removed outlier: 3.714A pdb=" N LYS I 592 " --> pdb=" O LEU I 588 " (cutoff:3.500A) Processing helix chain 'I' and resid 594 through 603 Processing helix chain 'J' and resid 24 through 32 Processing helix chain 'J' and resid 51 through 66 removed outlier: 3.551A pdb=" N ALA J 65 " --> pdb=" O ILE J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 90 Processing helix chain 'J' and resid 109 through 113 Processing helix chain 'J' and resid 155 through 171 removed outlier: 4.662A pdb=" N SER J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 180 Processing helix chain 'J' and resid 196 through 199 Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 401 through 413 Processing helix chain 'K' and resid 446 through 450 removed outlier: 4.104A pdb=" N SER K 449 " --> pdb=" O ASN K 446 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 486 removed outlier: 3.770A pdb=" N PHE K 474 " --> pdb=" O ASP K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 527 through 540 removed outlier: 3.614A pdb=" N LYS K 540 " --> pdb=" O GLU K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 553 removed outlier: 3.589A pdb=" N ALA K 545 " --> pdb=" O GLY K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 593 removed outlier: 3.788A pdb=" N LYS K 592 " --> pdb=" O LEU K 588 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR K 593 " --> pdb=" O SER K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 594 through 603 Processing helix chain 'L' and resid 471 through 487 Processing helix chain 'L' and resid 511 through 523 Processing helix chain 'L' and resid 527 through 540 Processing helix chain 'L' and resid 542 through 554 Processing helix chain 'L' and resid 572 through 591 Processing helix chain 'L' and resid 594 through 603 Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.150A pdb=" N LYS B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 47 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 42 removed outlier: 5.150A pdb=" N LYS B 46 " --> pdb=" O THR B 42 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 47 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 114 through 122 removed outlier: 4.039A pdb=" N ASP B 131 " --> pdb=" O ARG B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA9, first strand: chain 'C' and resid 114 through 122 Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB2, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.645A pdb=" N TYR D 9 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 114 through 122 removed outlier: 6.612A pdb=" N ARG D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU D 136 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER D 117 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS D 134 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS D 119 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR D 132 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG D 121 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 122 removed outlier: 6.419A pdb=" N ARG E 115 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU E 136 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N SER E 117 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS E 134 " --> pdb=" O SER E 117 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS E 119 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR E 132 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG E 121 " --> pdb=" O SER E 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 145 removed outlier: 3.771A pdb=" N TYR F 9 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 189 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 114 through 122 removed outlier: 6.415A pdb=" N ARG F 115 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU F 136 " --> pdb=" O ARG F 115 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER F 117 " --> pdb=" O LYS F 134 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS F 134 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS F 119 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR F 132 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG F 121 " --> pdb=" O SER F 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 59 through 61 removed outlier: 4.204A pdb=" N VAL G 122 " --> pdb=" O LYS G 2 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 59 through 61 removed outlier: 4.204A pdb=" N VAL G 122 " --> pdb=" O LYS G 2 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 102 Processing sheet with id=AC3, first strand: chain 'H' and resid 2 through 4 removed outlier: 6.583A pdb=" N SER H 14 " --> pdb=" O CYS H 29 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS H 29 " --> pdb=" O SER H 14 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 57 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS H 58 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 139 through 142 Processing sheet with id=AC5, first strand: chain 'H' and resid 251 through 254 removed outlier: 6.731A pdb=" N VAL H 225 " --> pdb=" O ILE H 311 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER H 313 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 434 through 436 removed outlier: 6.477A pdb=" N LYS H 434 " --> pdb=" O ILE H 466 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE H 468 " --> pdb=" O LYS H 434 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL H 436 " --> pdb=" O ILE H 468 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N ASP H 470 " --> pdb=" O VAL H 436 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG H 465 " --> pdb=" O LYS H 462 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 445 through 446 Processing sheet with id=AC8, first strand: chain 'I' and resid 436 through 437 removed outlier: 6.970A pdb=" N VAL I 436 " --> pdb=" O ILE I 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 451 through 454 removed outlier: 3.781A pdb=" N ARG I 451 " --> pdb=" O GLU L 461 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL L 436 " --> pdb=" O ILE L 468 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ASP L 470 " --> pdb=" O VAL L 436 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 457 through 458 Processing sheet with id=AD2, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD3, first strand: chain 'J' and resid 48 through 49 Processing sheet with id=AD4, first strand: chain 'J' and resid 114 through 122 removed outlier: 6.480A pdb=" N ARG J 115 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU J 136 " --> pdb=" O ARG J 115 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER J 117 " --> pdb=" O LYS J 134 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS J 134 " --> pdb=" O SER J 117 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS J 119 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR J 132 " --> pdb=" O HIS J 119 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG J 121 " --> pdb=" O SER J 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.683A pdb=" N TYR K 191 " --> pdb=" O ASN K 163 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU K 195 " --> pdb=" O SER K 167 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU K 418 " --> pdb=" O VAL K 393 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 445 through 447 877 hydrogen bonds defined for protein. 2526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4314 1.33 - 1.45: 6444 1.45 - 1.58: 12638 1.58 - 1.71: 176 1.71 - 1.83: 148 Bond restraints: 23720 Sorted by residual: bond pdb=" C THR J 109 " pdb=" N LYS J 110 " ideal model delta sigma weight residual 1.335 1.491 -0.156 1.31e-02 5.83e+03 1.42e+02 bond pdb=" C LEU J 177 " pdb=" N ASN J 178 " ideal model delta sigma weight residual 1.335 1.475 -0.140 1.38e-02 5.25e+03 1.03e+02 bond pdb=" C ASN H 522 " pdb=" N ILE H 523 " ideal model delta sigma weight residual 1.332 1.229 0.104 1.15e-02 7.56e+03 8.10e+01 bond pdb=" C ASN H 246 " pdb=" N PHE H 247 " ideal model delta sigma weight residual 1.330 1.208 0.122 1.37e-02 5.33e+03 7.96e+01 bond pdb=" C PHE G 51 " pdb=" N LEU G 52 " ideal model delta sigma weight residual 1.334 1.438 -0.103 1.27e-02 6.20e+03 6.64e+01 ... (remaining 23715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 30067 2.13 - 4.26: 1910 4.26 - 6.39: 297 6.39 - 8.53: 85 8.53 - 10.66: 20 Bond angle restraints: 32379 Sorted by residual: angle pdb=" N ILE H 523 " pdb=" CA ILE H 523 " pdb=" C ILE H 523 " ideal model delta sigma weight residual 112.90 104.98 7.92 9.60e-01 1.09e+00 6.81e+01 angle pdb=" O THR J 109 " pdb=" C THR J 109 " pdb=" N LYS J 110 " ideal model delta sigma weight residual 122.68 130.49 -7.81 1.17e+00 7.31e-01 4.46e+01 angle pdb=" CA MET K 508 " pdb=" C MET K 508 " pdb=" N SER K 509 " ideal model delta sigma weight residual 116.01 125.08 -9.07 1.41e+00 5.03e-01 4.13e+01 angle pdb=" C MET K 508 " pdb=" N SER K 509 " pdb=" CA SER K 509 " ideal model delta sigma weight residual 120.87 131.46 -10.59 1.69e+00 3.50e-01 3.92e+01 angle pdb=" CA ASN H 246 " pdb=" C ASN H 246 " pdb=" N PHE H 247 " ideal model delta sigma weight residual 114.76 121.73 -6.97 1.14e+00 7.69e-01 3.74e+01 ... (remaining 32374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 13936 35.57 - 71.14: 551 71.14 - 106.71: 54 106.71 - 142.28: 0 142.28 - 177.86: 3 Dihedral angle restraints: 14544 sinusoidal: 6643 harmonic: 7901 Sorted by residual: dihedral pdb=" O4' C N 2 " pdb=" C1' C N 2 " pdb=" N1 C N 2 " pdb=" C2 C N 2 " ideal model delta sinusoidal sigma weight residual 232.00 54.14 177.86 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C N -16 " pdb=" C1' C N -16 " pdb=" N1 C N -16 " pdb=" C2 C N -16 " ideal model delta sinusoidal sigma weight residual -128.00 48.47 -176.47 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U M 5 " pdb=" C1' U M 5 " pdb=" N1 U M 5 " pdb=" C2 U M 5 " ideal model delta sinusoidal sigma weight residual -128.00 44.43 -172.43 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 14541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3234 0.098 - 0.195: 444 0.195 - 0.293: 40 0.293 - 0.391: 11 0.391 - 0.488: 2 Chirality restraints: 3731 Sorted by residual: chirality pdb=" CB VAL H 460 " pdb=" CA VAL H 460 " pdb=" CG1 VAL H 460 " pdb=" CG2 VAL H 460 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CB ILE G 100 " pdb=" CA ILE G 100 " pdb=" CG1 ILE G 100 " pdb=" CG2 ILE G 100 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CB ILE G 163 " pdb=" CA ILE G 163 " pdb=" CG1 ILE G 163 " pdb=" CG2 ILE G 163 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 3728 not shown) Planarity restraints: 3835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 475 " -0.026 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" CG ASP H 475 " 0.096 2.00e-02 2.50e+03 pdb=" OD1 ASP H 475 " -0.035 2.00e-02 2.50e+03 pdb=" OD2 ASP H 475 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU F 68 " -0.028 2.00e-02 2.50e+03 5.36e-02 2.87e+01 pdb=" CD GLU F 68 " 0.093 2.00e-02 2.50e+03 pdb=" OE1 GLU F 68 " -0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU F 68 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 158 " -0.024 2.00e-02 2.50e+03 5.09e-02 2.60e+01 pdb=" CD GLU K 158 " 0.088 2.00e-02 2.50e+03 pdb=" OE1 GLU K 158 " -0.031 2.00e-02 2.50e+03 pdb=" OE2 GLU K 158 " -0.033 2.00e-02 2.50e+03 ... (remaining 3832 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 776 2.68 - 3.24: 21201 3.24 - 3.79: 38775 3.79 - 4.35: 53359 4.35 - 4.90: 85299 Nonbonded interactions: 199410 Sorted by model distance: nonbonded pdb=" OD2 ASP H 169 " pdb="ZN ZN H 701 " model vdw 2.128 2.230 nonbonded pdb=" OG SER G 68 " pdb=" OE1 GLU G 90 " model vdw 2.182 3.040 nonbonded pdb=" OG1 THR B 42 " pdb=" O ASN B 45 " model vdw 2.215 3.040 nonbonded pdb=" OG SER C 16 " pdb=" O GLY C 180 " model vdw 2.226 3.040 nonbonded pdb=" NH2 ARG L 530 " pdb=" OP1 C N 28 " model vdw 2.254 3.120 ... (remaining 199405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 154 or (resid 155 and (name N or name CA o \ r name C or name O or name CB )) or resid 156 through 192 or (resid 193 through \ 194 and (name N or name CA or name C or name O or name CB )) or resid 195 throug \ h 196 or resid 301)) selection = (chain 'C' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 111 through 123 or (resid 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125 through 154 or (re \ sid 155 and (name N or name CA or name C or name O or name CB )) or resid 156 th \ rough 192 or (resid 193 through 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 through 196 or resid 301)) selection = (chain 'D' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 111 through 123 or (resid 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125 through 154 or (re \ sid 155 and (name N or name CA or name C or name O or name CB )) or resid 156 th \ rough 192 or (resid 193 through 194 and (name N or name CA or name C or name O o \ r name CB )) or resid 195 through 196 or resid 301)) selection = (chain 'E' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 33 or (resid 34 through 35 and (name N or name CA \ or name C or name O or name CB )) or resid 36 through 74 or (resid 75 and (name \ N or name CA or name C or name O or name CB )) or resid 76 or (resid 77 through \ 79 and (name N or name CA or name C or name O or name CB )) or resid 80 through \ 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 94 or (resid 95 through 96 and (name N or name CA or name C or nam \ e O or name CB )) or resid 97 through 109 or (resid 110 and (name N or name CA o \ r name C or name O or name CB )) or resid 111 through 123 or (resid 124 and (nam \ e N or name CA or name C or name O or name CB )) or resid 125 through 154 or (re \ sid 155 and (name N or name CA or name C or name O or name CB )) or resid 156 th \ rough 196 or resid 301)) selection = (chain 'F' and (resid 3 through 33 or (resid 34 through 35 and (name N or name C \ A or name C or name O or name CB )) or resid 36 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB )) or resid 111 through 123 or ( \ resid 124 and (name N or name CA or name C or name O or name CB )) or resid 125 \ through 192 or (resid 193 through 194 and (name N or name CA or name C or name O \ or name CB )) or resid 195 through 196 or resid 301)) selection = (chain 'J' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 through 74 or (resid 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 or (resid 77 through 79 and (na \ me N or name CA or name C or name O or name CB )) or resid 80 through 82 or (res \ id 83 and (name N or name CA or name C or name O or name CB )) or resid 84 throu \ gh 94 or (resid 95 through 96 and (name N or name CA or name C or name O or name \ CB )) or resid 97 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 123 or (resid 124 and (name N or name \ CA or name C or name O or name CB )) or resid 125 through 154 or (resid 155 and \ (name N or name CA or name C or name O or name CB )) or resid 156 through 192 o \ r (resid 193 through 194 and (name N or name CA or name C or name O or name CB ) \ ) or resid 195 through 196 or resid 301)) } ncs_group { reference = (chain 'I' and (resid 435 through 488 or resid 506 through 539 or (resid 540 and \ (name N or name CA or name C or name O or name CB )) or resid 541 through 546 o \ r (resid 547 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 48 through 577 or (resid 578 and (name N or name CA or name C or name O or name \ CB )) or resid 579 through 596 or (resid 597 and (name N or name CA or name C or \ name O or name CB )) or resid 598 through 607)) selection = (chain 'L' and (resid 435 through 461 or (resid 462 and (name N or name CA or na \ me C or name O or name CB )) or resid 463 through 607)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 59.830 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.170 23720 Z= 0.576 Angle : 1.187 10.658 32379 Z= 0.721 Chirality : 0.070 0.488 3731 Planarity : 0.009 0.111 3835 Dihedral : 18.283 177.856 9424 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.37 % Favored : 94.25 % Rotamer: Outliers : 0.70 % Allowed : 18.07 % Favored : 81.22 % 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: -3.22 (0.14), residues: 2661 helix: -1.40 (0.15), residues: 875 sheet: -2.19 (0.21), residues: 496 loop : -2.64 (0.14), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 478 HIS 0.023 0.004 HIS H 373 PHE 0.056 0.004 PHE I 458 TYR 0.048 0.003 TYR G 141 ARG 0.021 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 386 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 116 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7770 (tp30) REVERT: C 189 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7828 (mttp) REVERT: F 156 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7618 (tptp) REVERT: G 141 TYR cc_start: 0.7985 (m-10) cc_final: 0.7722 (m-80) REVERT: G 195 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: I 568 GLU cc_start: 0.8183 (tt0) cc_final: 0.7608 (tt0) REVERT: J 5 MET cc_start: 0.8478 (mtm) cc_final: 0.8271 (mtp) REVERT: K 140 LYS cc_start: 0.7041 (mtpt) cc_final: 0.6050 (tptt) REVERT: L 462 LYS cc_start: 0.7088 (mttt) cc_final: 0.6541 (mttp) outliers start: 16 outliers final: 7 residues processed: 394 average time/residue: 0.4163 time to fit residues: 242.2371 Evaluate side-chains 358 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 350 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 453 MET Chi-restraints excluded: chain K residue 463 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 9.9990 chunk 206 optimal weight: 0.3980 chunk 114 optimal weight: 8.9990 chunk 70 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 119 HIS F 36 ASN G 99 ASN H 98 ASN H 107 ASN H 325 ASN I 443 ASN J 162 GLN ** K 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 563 ASN L 479 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.168808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.126658 restraints weight = 26244.580| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.54 r_work: 0.3174 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23720 Z= 0.181 Angle : 0.575 7.677 32379 Z= 0.307 Chirality : 0.042 0.292 3731 Planarity : 0.004 0.058 3835 Dihedral : 15.920 176.547 4289 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.80 % Favored : 96.02 % Rotamer: Outliers : 1.76 % Allowed : 17.33 % Favored : 80.91 % 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: -2.02 (0.15), residues: 2661 helix: 0.19 (0.17), residues: 892 sheet: -1.81 (0.21), residues: 504 loop : -2.29 (0.14), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 535 HIS 0.005 0.001 HIS H 373 PHE 0.021 0.001 PHE G 74 TYR 0.018 0.001 TYR G 137 ARG 0.005 0.001 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5322 Ramachandran restraints generated. 2661 Oldfield, 0 Emsley, 2661 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 375 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7654 (mtp) cc_final: 0.7419 (mtp) REVERT: A 51 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6711 (t80) REVERT: A 111 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: C 189 LYS cc_start: 0.8476 (mtpp) cc_final: 0.7706 (mttp) REVERT: D 196 ASP cc_start: 0.8371 (p0) cc_final: 0.8114 (p0) REVERT: E 79 ARG cc_start: 0.8395 (ptp-170) cc_final: 0.7684 (mmp-170) REVERT: E 122 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8640 (mt) REVERT: E 197 ARG cc_start: 0.8093 (ptp90) cc_final: 0.7860 (ptp90) REVERT: F 156 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7069 (tptp) REVERT: G 159 LYS cc_start: 0.7694 (mtpt) cc_final: 0.7315 (mtmt) REVERT: H 225 VAL cc_start: 0.5631 (OUTLIER) cc_final: 0.5410 (p) REVERT: H 247 PHE cc_start: 0.5668 (t80) cc_final: 0.5151 (t80) REVERT: H 453 MET cc_start: 0.8010 (ttp) cc_final: 0.7684 (ptm) REVERT: I 453 MET cc_start: 0.8675 (ttp) cc_final: 0.8433 (ttp) REVERT: I 568 GLU cc_start: 0.8280 (tt0) cc_final: 0.7848 (tt0) REVERT: I 592 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8112 (ttmt) REVERT: J 5 MET cc_start: 0.8406 (mtm) cc_final: 0.8147 (mtp) REVERT: K 140 LYS cc_start: 0.6706 (mtpt) cc_final: 0.5636 (tttp) REVERT: K 551 GLN cc_start: 0.7965 (tt0) cc_final: 0.7578 (tm-30) REVERT: L 532 LYS cc_start: 0.6714 (ttpp) cc_final: 0.6215 (ttpt) REVERT: L 551 GLN cc_start: 0.7896 (tt0) cc_final: 0.7352 (tp40) outliers start: 40 outliers final: 16 residues processed: 395 average time/residue: 0.4236 time to fit residues: 247.8989 Evaluate side-chains 356 residues out of total 2413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 336 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 PHE Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain H residue 188 ASN Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain I residue 445 CYS Chi-restraints excluded: chain I residue 467 GLU Chi-restraints excluded: chain I residue 477 ILE Chi-restraints excluded: chain I residue 508 MET Chi-restraints excluded: chain L residue 470 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 50.5059 > 50: distance: 75 - 102: 3.757 distance: 81 - 110: 5.630 distance: 86 - 118: 4.460 distance: 90 - 91: 3.708 distance: 91 - 92: 6.861 distance: 91 - 94: 4.119 distance: 92 - 93: 4.407 distance: 92 - 102: 9.214 distance: 94 - 95: 8.009 distance: 95 - 96: 3.734 distance: 95 - 97: 4.671 distance: 96 - 98: 5.775 distance: 97 - 99: 5.110 distance: 98 - 100: 5.228 distance: 99 - 100: 5.580 distance: 100 - 101: 6.869 distance: 102 - 103: 7.554 distance: 103 - 104: 7.681 distance: 103 - 106: 14.409 distance: 104 - 105: 5.758 distance: 104 - 110: 6.335 distance: 106 - 107: 12.302 distance: 107 - 108: 3.596 distance: 107 - 109: 7.200 distance: 110 - 111: 5.328 distance: 111 - 112: 3.928 distance: 111 - 114: 11.593 distance: 112 - 113: 10.305 distance: 112 - 118: 8.674 distance: 114 - 115: 7.439 distance: 114 - 116: 18.113 distance: 115 - 117: 7.888 distance: 119 - 120: 4.101 distance: 119 - 122: 4.112 distance: 120 - 121: 11.504 distance: 120 - 126: 4.960 distance: 122 - 123: 11.135 distance: 123 - 124: 11.108 distance: 123 - 125: 15.456 distance: 126 - 127: 3.583 distance: 127 - 128: 5.916 distance: 127 - 130: 7.350 distance: 128 - 129: 8.294 distance: 128 - 134: 5.035 distance: 130 - 131: 3.685 distance: 130 - 132: 14.299 distance: 131 - 133: 8.665 distance: 134 - 135: 4.288 distance: 135 - 136: 3.589 distance: 135 - 138: 6.384 distance: 136 - 137: 9.338 distance: 136 - 142: 5.893 distance: 138 - 139: 10.087 distance: 139 - 140: 7.172 distance: 139 - 141: 10.896 distance: 142 - 143: 4.161 distance: 143 - 146: 5.986 distance: 144 - 145: 12.540 distance: 144 - 153: 10.138 distance: 146 - 147: 5.881 distance: 147 - 148: 3.959 distance: 147 - 149: 8.791 distance: 148 - 150: 6.195 distance: 149 - 151: 6.104 distance: 150 - 152: 7.273 distance: 151 - 152: 7.319 distance: 153 - 154: 20.290 distance: 154 - 155: 9.521 distance: 154 - 157: 5.187 distance: 155 - 156: 16.384 distance: 155 - 161: 23.338 distance: 157 - 158: 6.666 distance: 158 - 159: 7.076 distance: 158 - 160: 22.003 distance: 161 - 162: 40.923 distance: 161 - 167: 42.611 distance: 162 - 163: 11.308 distance: 162 - 165: 19.566 distance: 163 - 164: 9.985 distance: 163 - 168: 7.162 distance: 165 - 166: 24.916 distance: 166 - 167: 24.494 distance: 168 - 169: 14.956 distance: 169 - 170: 8.593 distance: 169 - 172: 18.275 distance: 170 - 171: 4.770 distance: 170 - 173: 5.435