Starting phenix.real_space_refine on Tue Jun 24 16:30:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8red_19083/06_2025/8red_19083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8red_19083/06_2025/8red_19083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8red_19083/06_2025/8red_19083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8red_19083/06_2025/8red_19083.map" model { file = "/net/cci-nas-00/data/ceres_data/8red_19083/06_2025/8red_19083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8red_19083/06_2025/8red_19083.cif" } resolution = 3.9 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 105 5.49 5 Mg 1 5.21 5 S 101 5.16 5 C 17785 2.51 5 N 5115 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28878 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "R" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "T" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1051 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9654 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 721 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 31, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 462 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2337 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 135 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16833 SG CYS D 70 106.207 113.798 91.476 1.00 46.98 S ATOM 16962 SG CYS D 88 105.029 115.022 94.292 1.00 36.36 S ATOM 23075 SG CYS D 898 100.706 46.830 88.144 1.00 20.87 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.29 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.29 Time building chain proxies: 16.20, per 1000 atoms: 0.56 Number of scatterers: 28878 At special positions: 0 Unit cell: (142.576, 170.448, 168.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 101 16.00 P 105 15.00 Mg 1 11.99 O 5769 8.00 N 5115 7.00 C 17785 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: 7.21 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 43 sheets defined 39.8% alpha, 14.2% beta 41 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 10.14 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.740A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.841A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.118A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.647A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.881A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.681A pdb=" N LEU A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 290' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.669A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.810A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.649A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.757A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.721A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.805A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.659A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.518A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.536A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.734A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.633A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 4.084A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 294' Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.572A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.917A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.572A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.489A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.519A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.980A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.607A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.661A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.744A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 3.927A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.975A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.605A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1299 through 1311 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.769A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 14 removed outlier: 4.115A pdb=" N THR D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 4.098A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.902A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.245A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 4.101A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.573A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.786A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.590A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.833A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.796A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.598A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.713A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.722A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.621A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.145A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.555A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.677A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.314A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.636A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.865A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 Processing helix chain 'M' and resid 134 through 146 Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 183 Processing helix chain 'M' and resid 194 through 205 removed outlier: 4.172A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.171A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 232 through 240 removed outlier: 3.853A pdb=" N MET M 236 " --> pdb=" O PHE M 232 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 256 removed outlier: 3.671A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU M 256 " --> pdb=" O LEU M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 351 removed outlier: 4.187A pdb=" N ASP M 338 " --> pdb=" O GLU M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.729A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 4.046A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 429 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.843A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 9.049A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 111 removed outlier: 3.668A pdb=" N GLY A 106 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA A 138 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLY A 108 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N GLU A 136 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 11.798A pdb=" N VAL A 110 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 134 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.535A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.534A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.565A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.815A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.709A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.709A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.514A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.089A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.782A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.862A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.715A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.808A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.477A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 841 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.983A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.157A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.612A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.958A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 525 through 527 removed outlier: 6.600A pdb=" N MET D 525 " --> pdb=" O LYS D 549 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ARG D 551 " --> pdb=" O MET D 525 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.776A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 957 through 958 Processing sheet with id=AE3, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.533A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1059 through 1062 removed outlier: 3.793A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 4.552A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE7, first strand: chain 'M' and resid 287 through 289 1127 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 14.97 Time building geometry restraints manager: 8.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8823 1.33 - 1.45: 4467 1.45 - 1.58: 15832 1.58 - 1.70: 211 1.70 - 1.82: 175 Bond restraints: 29508 Sorted by residual: bond pdb=" CG PRO C 567 " pdb=" CD PRO C 567 " ideal model delta sigma weight residual 1.503 1.362 0.141 3.40e-02 8.65e+02 1.71e+01 bond pdb=" CB PRO A 251 " pdb=" CG PRO A 251 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.16e+01 bond pdb=" CB PRO C 567 " pdb=" CG PRO C 567 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.76e+00 bond pdb=" N PRO C 567 " pdb=" CA PRO C 567 " ideal model delta sigma weight residual 1.473 1.433 0.040 1.32e-02 5.74e+03 9.10e+00 bond pdb=" C GLU M 268 " pdb=" N PRO M 269 " ideal model delta sigma weight residual 1.333 1.363 -0.029 1.01e-02 9.80e+03 8.33e+00 ... (remaining 29503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 40421 4.58 - 9.17: 84 9.17 - 13.75: 9 13.75 - 18.33: 3 18.33 - 22.92: 1 Bond angle restraints: 40518 Sorted by residual: angle pdb=" CA PRO C 567 " pdb=" N PRO C 567 " pdb=" CD PRO C 567 " ideal model delta sigma weight residual 112.00 94.88 17.12 1.40e+00 5.10e-01 1.50e+02 angle pdb=" CA PRO D1139 " pdb=" N PRO D1139 " pdb=" CD PRO D1139 " ideal model delta sigma weight residual 112.00 96.40 15.60 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CA PRO A 251 " pdb=" N PRO A 251 " pdb=" CD PRO A 251 " ideal model delta sigma weight residual 112.00 97.20 14.80 1.40e+00 5.10e-01 1.12e+02 angle pdb=" CA PRO C 375 " pdb=" N PRO C 375 " pdb=" CD PRO C 375 " ideal model delta sigma weight residual 112.00 101.42 10.58 1.40e+00 5.10e-01 5.71e+01 angle pdb=" N PRO C 567 " pdb=" CD PRO C 567 " pdb=" CG PRO C 567 " ideal model delta sigma weight residual 103.20 93.56 9.64 1.50e+00 4.44e-01 4.13e+01 ... (remaining 40513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 16729 35.55 - 71.09: 952 71.09 - 106.64: 51 106.64 - 142.18: 1 142.18 - 177.73: 3 Dihedral angle restraints: 17736 sinusoidal: 7342 harmonic: 10394 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 143.03 36.97 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CA ILE D 416 " pdb=" C ILE D 416 " pdb=" N ARG D 417 " pdb=" CA ARG D 417 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 17733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3621 0.044 - 0.088: 904 0.088 - 0.133: 267 0.133 - 0.177: 14 0.177 - 0.221: 2 Chirality restraints: 4808 Sorted by residual: chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" P C R 0 " pdb=" OP1 C R 0 " pdb=" OP2 C R 0 " pdb=" O5' C R 0 " both_signs ideal model delta sigma weight residual True 2.41 -2.60 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CA PRO C1062 " pdb=" N PRO C1062 " pdb=" C PRO C1062 " pdb=" CB PRO C1062 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 4805 not shown) Planarity restraints: 4943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.162 5.00e-02 4.00e+02 2.25e-01 8.07e+01 pdb=" N PRO D1139 " -0.386 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.137 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " -0.145 5.00e-02 4.00e+02 2.01e-01 6.49e+01 pdb=" N PRO C 567 " 0.347 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " -0.112 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 250 " -0.100 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO A 251 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.072 5.00e-02 4.00e+02 ... (remaining 4940 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 425 2.65 - 3.21: 26847 3.21 - 3.78: 44241 3.78 - 4.34: 56958 4.34 - 4.90: 93924 Nonbonded interactions: 222395 Sorted by model distance: nonbonded pdb=" O LEU D 71 " pdb="ZN ZN D1502 " model vdw 2.088 2.230 nonbonded pdb=" O PRO B 179 " pdb=" OG1 THR B 207 " model vdw 2.176 3.040 nonbonded pdb=" O LEU D 363 " pdb=" OG SER D 486 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP C 654 " pdb=" NE2 GLN C 659 " model vdw 2.186 3.120 nonbonded pdb=" NH2 ARG C 528 " pdb=" O SER C 576 " model vdw 2.191 3.120 ... (remaining 222390 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=0.00 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: 0.460 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: 1.240 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 80.050 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.120 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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 : 0.005 0.170 29511 Z= 0.186 Angle : 0.682 22.919 40518 Z= 0.358 Chirality : 0.042 0.221 4808 Planarity : 0.007 0.225 4943 Dihedral : 19.760 177.728 11030 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.54 % Rotamer: Outliers : 0.41 % Allowed : 29.69 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.58 (0.14), residues: 3589 helix: 0.90 (0.15), residues: 1282 sheet: 0.49 (0.26), residues: 377 loop : -1.52 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP M 212 HIS 0.005 0.001 HIS D 430 PHE 0.018 0.001 PHE D 7 TYR 0.012 0.001 TYR D 631 ARG 0.016 0.000 ARG D1149 Details of bonding type rmsd hydrogen bonds : bond 0.16399 ( 1213) hydrogen bonds : angle 5.83389 ( 3404) metal coordination : bond 0.00205 ( 3) covalent geometry : bond 0.00468 (29508) covalent geometry : angle 0.68165 (40518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 270 time to evaluate : 4.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.7391 (ttp) cc_final: 0.7149 (ttt) REVERT: M 193 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7917 (mttt) REVERT: M 280 LYS cc_start: 0.6541 (pttm) cc_final: 0.5493 (tppt) REVERT: M 346 CYS cc_start: 0.8325 (m) cc_final: 0.7868 (p) REVERT: M 354 PHE cc_start: 0.7567 (t80) cc_final: 0.7201 (t80) REVERT: M 365 MET cc_start: 0.3420 (tmm) cc_final: 0.3079 (tpt) REVERT: M 406 HIS cc_start: 0.6298 (m90) cc_final: 0.5596 (m-70) REVERT: M 426 LYS cc_start: 0.7437 (pttm) cc_final: 0.7159 (ptpt) outliers start: 11 outliers final: 1 residues processed: 278 average time/residue: 0.5001 time to fit residues: 223.4560 Evaluate side-chains 184 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 3.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 0.0060 chunk 278 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 0.0020 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 175 optimal weight: 0.0570 chunk 214 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 450 HIS ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN M 262 GLN M 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.054165 restraints weight = 126199.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055617 restraints weight = 67225.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.056562 restraints weight = 44981.266| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29511 Z= 0.117 Angle : 0.594 10.905 40518 Z= 0.304 Chirality : 0.041 0.177 4808 Planarity : 0.005 0.144 4943 Dihedral : 16.407 178.253 5075 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.40 % Allowed : 27.41 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.37 (0.14), residues: 3589 helix: 1.00 (0.15), residues: 1335 sheet: 0.68 (0.26), residues: 389 loop : -1.44 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 126 HIS 0.002 0.001 HIS C1116 PHE 0.016 0.001 PHE M 355 TYR 0.016 0.001 TYR A 277 ARG 0.010 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 1213) hydrogen bonds : angle 4.39322 ( 3404) metal coordination : bond 0.00176 ( 3) covalent geometry : bond 0.00259 (29508) covalent geometry : angle 0.59374 (40518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 211 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8586 (tp) REVERT: A 277 TYR cc_start: 0.7868 (m-80) cc_final: 0.7642 (m-80) REVERT: B 25 LYS cc_start: 0.9151 (ttmm) cc_final: 0.8886 (ttmm) REVERT: B 27 THR cc_start: 0.9575 (OUTLIER) cc_final: 0.9184 (p) REVERT: B 174 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7672 (t70) REVERT: C 62 TYR cc_start: 0.7706 (p90) cc_final: 0.7327 (p90) REVERT: C 685 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8816 (mtm) REVERT: C 785 ASP cc_start: 0.8166 (p0) cc_final: 0.7857 (p0) REVERT: C 813 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7340 (mm-30) REVERT: C 826 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8115 (t0) REVERT: C 853 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7200 (p0) REVERT: C 903 ARG cc_start: 0.8641 (mtt180) cc_final: 0.8354 (mmt-90) REVERT: C 908 GLU cc_start: 0.8851 (mp0) cc_final: 0.8521 (tp30) REVERT: C 1029 LEU cc_start: 0.9470 (tp) cc_final: 0.8857 (pp) REVERT: C 1085 MET cc_start: 0.9271 (mmm) cc_final: 0.9005 (mmm) REVERT: C 1131 MET cc_start: 0.8906 (tpp) cc_final: 0.8705 (tpp) REVERT: D 29 MET cc_start: 0.8851 (mmm) cc_final: 0.8054 (tmm) REVERT: D 698 MET cc_start: 0.9267 (mmm) cc_final: 0.8973 (mmt) REVERT: D 725 MET cc_start: 0.9213 (mtm) cc_final: 0.8696 (mtm) REVERT: D 821 MET cc_start: 0.9134 (tpp) cc_final: 0.8784 (tpp) REVERT: D 1366 HIS cc_start: 0.9328 (OUTLIER) cc_final: 0.8956 (m-70) REVERT: M 212 TRP cc_start: 0.8377 (m100) cc_final: 0.8137 (m100) REVERT: M 262 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7954 (pp30) REVERT: M 280 LYS cc_start: 0.7351 (pttm) cc_final: 0.6684 (tppt) REVERT: M 346 CYS cc_start: 0.8641 (m) cc_final: 0.8123 (p) REVERT: M 391 HIS cc_start: 0.7307 (t70) cc_final: 0.7064 (t70) REVERT: M 406 HIS cc_start: 0.6943 (m90) cc_final: 0.6222 (m-70) REVERT: M 425 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8383 (mmtt) REVERT: M 426 LYS cc_start: 0.7110 (pttm) cc_final: 0.6898 (ptpt) outliers start: 91 outliers final: 33 residues processed: 290 average time/residue: 0.4621 time to fit residues: 224.8274 Evaluate side-chains 225 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 262 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 268 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 chunk 276 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 348 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 148 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN D1367 GLN M 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.077238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052330 restraints weight = 127839.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053730 restraints weight = 68733.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.054625 restraints weight = 46499.196| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29511 Z= 0.189 Angle : 0.595 8.436 40518 Z= 0.307 Chirality : 0.041 0.184 4808 Planarity : 0.005 0.118 4943 Dihedral : 16.409 178.960 5071 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.81 % Allowed : 27.30 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.24 (0.14), residues: 3589 helix: 1.22 (0.15), residues: 1337 sheet: 0.61 (0.26), residues: 391 loop : -1.42 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 285 HIS 0.003 0.001 HIS A 66 PHE 0.015 0.001 PHE M 355 TYR 0.019 0.001 TYR D1232 ARG 0.009 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 1213) hydrogen bonds : angle 4.23516 ( 3404) metal coordination : bond 0.00362 ( 3) covalent geometry : bond 0.00420 (29508) covalent geometry : angle 0.59489 (40518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 188 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 VAL cc_start: 0.9604 (t) cc_final: 0.9400 (p) REVERT: A 253 LEU cc_start: 0.8887 (mp) cc_final: 0.8609 (tp) REVERT: A 277 TYR cc_start: 0.7828 (m-80) cc_final: 0.7563 (m-80) REVERT: B 25 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8873 (ttmm) REVERT: B 27 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9189 (p) REVERT: C 47 TYR cc_start: 0.8961 (OUTLIER) cc_final: 0.6845 (m-80) REVERT: C 239 MET cc_start: 0.7102 (mmm) cc_final: 0.6469 (mmm) REVERT: C 685 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8794 (mtm) REVERT: C 813 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7468 (mm-30) REVERT: C 826 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8219 (t0) REVERT: C 853 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7175 (p0) REVERT: C 903 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8326 (mmt180) REVERT: C 951 MET cc_start: 0.9103 (tmm) cc_final: 0.8770 (tmm) REVERT: C 1085 MET cc_start: 0.9352 (mmm) cc_final: 0.9084 (mmm) REVERT: C 1131 MET cc_start: 0.8989 (tpp) cc_final: 0.8769 (tpp) REVERT: C 1304 MET cc_start: 0.9477 (tpt) cc_final: 0.9147 (tpp) REVERT: D 29 MET cc_start: 0.8962 (mmm) cc_final: 0.8029 (tmm) REVERT: D 130 MET cc_start: 0.8350 (mmm) cc_final: 0.7998 (mmt) REVERT: D 698 MET cc_start: 0.9296 (mmm) cc_final: 0.9037 (mmm) REVERT: D 725 MET cc_start: 0.9215 (mtm) cc_final: 0.8798 (mtm) REVERT: D 747 MET cc_start: 0.8314 (ppp) cc_final: 0.8037 (ppp) REVERT: D 1249 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8738 (t0) REVERT: D 1366 HIS cc_start: 0.9359 (OUTLIER) cc_final: 0.9004 (m-70) REVERT: M 125 MET cc_start: 0.9084 (mmt) cc_final: 0.8833 (mmm) REVERT: M 130 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8851 (mm) REVERT: M 280 LYS cc_start: 0.7300 (pttm) cc_final: 0.6657 (tppt) REVERT: M 346 CYS cc_start: 0.8630 (m) cc_final: 0.8137 (p) REVERT: M 365 MET cc_start: 0.3492 (mmm) cc_final: 0.2691 (mmm) REVERT: M 425 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8476 (mmtt) outliers start: 102 outliers final: 44 residues processed: 276 average time/residue: 0.3673 time to fit residues: 171.9657 Evaluate side-chains 228 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 172 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 39 optimal weight: 0.1980 chunk 44 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.078429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053569 restraints weight = 127814.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.054980 restraints weight = 69036.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055836 restraints weight = 46807.591| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29511 Z= 0.105 Angle : 0.548 7.738 40518 Z= 0.282 Chirality : 0.041 0.234 4808 Planarity : 0.004 0.100 4943 Dihedral : 16.355 177.836 5071 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.17 % Allowed : 27.86 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.12 (0.14), residues: 3589 helix: 1.33 (0.15), residues: 1334 sheet: 0.74 (0.26), residues: 381 loop : -1.36 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 212 HIS 0.002 0.000 HIS M 406 PHE 0.010 0.001 PHE C1270 TYR 0.020 0.001 TYR D1232 ARG 0.008 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03076 ( 1213) hydrogen bonds : angle 4.02357 ( 3404) metal coordination : bond 0.00132 ( 3) covalent geometry : bond 0.00230 (29508) covalent geometry : angle 0.54840 (40518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 188 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 VAL cc_start: 0.9604 (t) cc_final: 0.9404 (p) REVERT: A 253 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 277 TYR cc_start: 0.7848 (m-80) cc_final: 0.7532 (m-80) REVERT: B 27 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9186 (p) REVERT: B 200 LYS cc_start: 0.9069 (tttt) cc_final: 0.8798 (ttpp) REVERT: B 205 MET cc_start: 0.8502 (tpp) cc_final: 0.8296 (tpp) REVERT: C 101 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8289 (mtm110) REVERT: C 239 MET cc_start: 0.7285 (mmm) cc_final: 0.6534 (mmm) REVERT: C 488 MET cc_start: 0.7867 (mmt) cc_final: 0.7415 (mtp) REVERT: C 523 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8377 (mt-10) REVERT: C 685 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8722 (mtm) REVERT: C 813 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 826 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8147 (t0) REVERT: C 903 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8258 (mtt-85) REVERT: C 951 MET cc_start: 0.9071 (tmm) cc_final: 0.8761 (tmm) REVERT: C 1085 MET cc_start: 0.9274 (mmm) cc_final: 0.8965 (mmm) REVERT: C 1265 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.8010 (t80) REVERT: C 1304 MET cc_start: 0.9383 (tpt) cc_final: 0.9154 (tpp) REVERT: D 29 MET cc_start: 0.8882 (mmm) cc_final: 0.8460 (mmm) REVERT: D 725 MET cc_start: 0.9164 (mtm) cc_final: 0.8701 (mtm) REVERT: D 747 MET cc_start: 0.8200 (ppp) cc_final: 0.7985 (ppp) REVERT: D 821 MET cc_start: 0.9161 (tpp) cc_final: 0.8899 (tpp) REVERT: D 1263 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7882 (tmtt) REVERT: D 1366 HIS cc_start: 0.9377 (OUTLIER) cc_final: 0.9064 (m-70) REVERT: E 30 MET cc_start: 0.8677 (mtp) cc_final: 0.8339 (mtt) REVERT: M 125 MET cc_start: 0.9039 (mmt) cc_final: 0.8767 (mmm) REVERT: M 130 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8749 (mm) REVERT: M 280 LYS cc_start: 0.7322 (pttm) cc_final: 0.6702 (tppt) REVERT: M 346 CYS cc_start: 0.8601 (m) cc_final: 0.8133 (p) REVERT: M 425 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8457 (mmtt) outliers start: 85 outliers final: 46 residues processed: 260 average time/residue: 0.3732 time to fit residues: 164.0635 Evaluate side-chains 234 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 179 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1263 LYS Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 426 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 261 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 324 optimal weight: 10.0000 chunk 59 optimal weight: 30.0000 chunk 245 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 239 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 437 ASN C 856 ASN D 158 GLN D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.076228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051338 restraints weight = 128955.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.052686 restraints weight = 70494.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053550 restraints weight = 48232.271| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29511 Z= 0.189 Angle : 0.585 8.859 40518 Z= 0.303 Chirality : 0.041 0.275 4808 Planarity : 0.004 0.087 4943 Dihedral : 16.371 179.178 5071 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.96 % Allowed : 27.45 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.11 (0.14), residues: 3589 helix: 1.34 (0.15), residues: 1339 sheet: 0.67 (0.26), residues: 383 loop : -1.34 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 126 HIS 0.003 0.001 HIS A 276 PHE 0.020 0.001 PHE M 355 TYR 0.020 0.001 TYR D1232 ARG 0.007 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 1213) hydrogen bonds : angle 4.08920 ( 3404) metal coordination : bond 0.00432 ( 3) covalent geometry : bond 0.00418 (29508) covalent geometry : angle 0.58541 (40518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 178 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8590 (tp) REVERT: A 277 TYR cc_start: 0.7870 (m-80) cc_final: 0.7531 (m-80) REVERT: B 25 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8760 (mmmt) REVERT: B 27 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9189 (p) REVERT: B 211 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8966 (mm) REVERT: C 62 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7500 (p90) REVERT: C 239 MET cc_start: 0.7567 (mmm) cc_final: 0.7036 (mmm) REVERT: C 488 MET cc_start: 0.7957 (mmt) cc_final: 0.7440 (mtp) REVERT: C 685 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8873 (mtm) REVERT: C 813 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7841 (mm-30) REVERT: C 853 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7336 (p0) REVERT: C 951 MET cc_start: 0.9116 (tmm) cc_final: 0.8847 (tmm) REVERT: C 1085 MET cc_start: 0.9282 (mmm) cc_final: 0.9038 (mmm) REVERT: C 1265 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8153 (t80) REVERT: C 1304 MET cc_start: 0.9470 (tpt) cc_final: 0.9225 (tpp) REVERT: D 29 MET cc_start: 0.8930 (mmm) cc_final: 0.8064 (mmm) REVERT: D 716 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8250 (pt0) REVERT: D 785 ASP cc_start: 0.8357 (t0) cc_final: 0.8052 (t0) REVERT: D 821 MET cc_start: 0.9128 (tpp) cc_final: 0.8927 (tpp) REVERT: D 822 MET cc_start: 0.8202 (ttp) cc_final: 0.7987 (ttt) REVERT: D 1263 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7987 (tmtt) REVERT: D 1366 HIS cc_start: 0.9344 (OUTLIER) cc_final: 0.9032 (m-70) REVERT: E 30 MET cc_start: 0.8705 (mtp) cc_final: 0.8373 (mtt) REVERT: M 130 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8848 (mm) REVERT: M 280 LYS cc_start: 0.7313 (pttm) cc_final: 0.6655 (tppt) REVERT: M 346 CYS cc_start: 0.8624 (m) cc_final: 0.8147 (p) REVERT: M 425 LYS cc_start: 0.8807 (mmtt) cc_final: 0.8477 (mmtt) outliers start: 106 outliers final: 65 residues processed: 271 average time/residue: 0.3817 time to fit residues: 174.7361 Evaluate side-chains 249 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1263 LYS Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 128 optimal weight: 5.9990 chunk 364 optimal weight: 30.0000 chunk 309 optimal weight: 20.0000 chunk 175 optimal weight: 6.9990 chunk 246 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 271 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 180 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C1136 GLN D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.075958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051099 restraints weight = 129118.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052437 restraints weight = 70404.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053307 restraints weight = 48172.296| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 29511 Z= 0.169 Angle : 0.574 8.823 40518 Z= 0.297 Chirality : 0.041 0.176 4808 Planarity : 0.004 0.080 4943 Dihedral : 16.365 179.082 5071 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.22 % Allowed : 27.41 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.09 (0.14), residues: 3589 helix: 1.36 (0.15), residues: 1340 sheet: 0.65 (0.26), residues: 387 loop : -1.34 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 126 HIS 0.003 0.001 HIS D 430 PHE 0.017 0.001 PHE M 355 TYR 0.021 0.001 TYR D1232 ARG 0.007 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 1213) hydrogen bonds : angle 4.05755 ( 3404) metal coordination : bond 0.00401 ( 3) covalent geometry : bond 0.00375 (29508) covalent geometry : angle 0.57399 (40518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 174 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 277 TYR cc_start: 0.7886 (m-80) cc_final: 0.7603 (m-80) REVERT: B 27 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9140 (p) REVERT: B 211 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8970 (mm) REVERT: C 62 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7514 (p90) REVERT: C 239 MET cc_start: 0.7540 (mmm) cc_final: 0.7072 (mmm) REVERT: C 488 MET cc_start: 0.7956 (mmt) cc_final: 0.7397 (mtp) REVERT: C 853 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7157 (p0) REVERT: C 951 MET cc_start: 0.9113 (tmm) cc_final: 0.8847 (tmm) REVERT: C 1085 MET cc_start: 0.9263 (mmm) cc_final: 0.9010 (mmm) REVERT: C 1131 MET cc_start: 0.8748 (tpp) cc_final: 0.8524 (tpp) REVERT: C 1253 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8684 (mm) REVERT: D 29 MET cc_start: 0.8926 (mmm) cc_final: 0.7997 (mmm) REVERT: D 133 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8625 (ttm-80) REVERT: D 747 MET cc_start: 0.8177 (ppp) cc_final: 0.7802 (ppp) REVERT: D 785 ASP cc_start: 0.8422 (t0) cc_final: 0.8117 (t0) REVERT: D 1366 HIS cc_start: 0.9343 (OUTLIER) cc_final: 0.9024 (m-70) REVERT: E 30 MET cc_start: 0.8731 (mtp) cc_final: 0.8465 (mtt) REVERT: M 125 MET cc_start: 0.9084 (mmt) cc_final: 0.8809 (mmm) REVERT: M 130 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8813 (mm) REVERT: M 280 LYS cc_start: 0.7306 (pttm) cc_final: 0.6648 (tppt) outliers start: 113 outliers final: 72 residues processed: 273 average time/residue: 0.3798 time to fit residues: 173.4083 Evaluate side-chains 248 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 167 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 62.0951 > 50: distance: 33 - 98: 17.633 distance: 36 - 95: 19.925 distance: 58 - 63: 9.482 distance: 63 - 64: 10.587 distance: 64 - 65: 20.841 distance: 64 - 67: 13.821 distance: 65 - 66: 12.888 distance: 65 - 74: 32.776 distance: 67 - 68: 15.788 distance: 68 - 69: 3.299 distance: 74 - 75: 17.080 distance: 75 - 76: 44.159 distance: 75 - 78: 12.919 distance: 76 - 77: 17.416 distance: 76 - 85: 45.888 distance: 78 - 79: 23.914 distance: 79 - 80: 8.601 distance: 80 - 81: 7.348 distance: 81 - 82: 6.682 distance: 82 - 83: 3.855 distance: 82 - 84: 4.195 distance: 85 - 86: 36.101 distance: 86 - 87: 20.585 distance: 86 - 89: 35.150 distance: 87 - 88: 18.029 distance: 87 - 90: 31.793 distance: 90 - 91: 39.291 distance: 91 - 92: 30.102 distance: 91 - 94: 25.271 distance: 92 - 93: 35.003 distance: 95 - 96: 16.462 distance: 96 - 97: 22.856 distance: 96 - 99: 46.006 distance: 97 - 98: 30.829 distance: 97 - 103: 51.113 distance: 99 - 100: 18.432 distance: 100 - 101: 42.266 distance: 100 - 102: 26.770 distance: 103 - 104: 20.318 distance: 103 - 109: 11.527 distance: 104 - 105: 11.518 distance: 104 - 107: 19.329 distance: 105 - 106: 23.652 distance: 105 - 110: 14.725 distance: 107 - 108: 10.443 distance: 108 - 109: 24.721 distance: 110 - 111: 20.840 distance: 111 - 112: 19.408 distance: 111 - 114: 23.413 distance: 112 - 113: 27.335 distance: 112 - 115: 27.546 distance: 113 - 138: 7.659 distance: 115 - 116: 15.730 distance: 116 - 117: 28.230 distance: 116 - 119: 10.151 distance: 117 - 118: 23.639 distance: 117 - 122: 43.384 distance: 118 - 145: 19.231 distance: 119 - 120: 32.760 distance: 119 - 121: 12.159 distance: 122 - 123: 26.431 distance: 123 - 124: 27.743 distance: 123 - 126: 25.330 distance: 124 - 125: 39.940 distance: 124 - 130: 24.993 distance: 125 - 150: 29.415 distance: 126 - 127: 17.035 distance: 126 - 128: 35.557 distance: 127 - 129: 32.732 distance: 130 - 131: 17.609 distance: 131 - 132: 32.124 distance: 131 - 134: 21.847 distance: 132 - 133: 22.508 distance: 132 - 138: 18.261 distance: 134 - 135: 14.393 distance: 134 - 136: 25.500 distance: 135 - 137: 26.835