Starting phenix.real_space_refine on Wed Jun 25 06:55:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kin_22888/06_2025/7kin_22888.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kin_22888/06_2025/7kin_22888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kin_22888/06_2025/7kin_22888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kin_22888/06_2025/7kin_22888.map" model { file = "/net/cci-nas-00/data/ceres_data/7kin_22888/06_2025/7kin_22888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kin_22888/06_2025/7kin_22888.cif" } resolution = 2.74 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= 0.004 sd= 0.119 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 103 5.49 5 Mg 1 5.21 5 S 99 5.16 5 C 18088 2.51 5 N 5245 2.21 5 O 5841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29379 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1716 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1765 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 8606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8606 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1048} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 9914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1270, 9914 Classifications: {'peptide': 1270} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1209} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 76} Chain: "F" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2510 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 308} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 870 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "O" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1096 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Chain: "P" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1009 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain breaks: 1 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 19155 SG CYS D 891 113.862 106.506 104.585 1.00 82.59 S ATOM 19722 SG CYS D 968 110.008 106.339 103.400 1.00 77.13 S ATOM 19764 SG CYS D 975 111.101 104.370 106.584 1.00 69.45 S ATOM 19782 SG CYS D 978 110.844 107.992 106.799 1.00 72.19 S ATOM 12593 SG CYS D 60 80.152 59.702 68.066 1.00102.84 S ATOM 12611 SG CYS D 62 78.677 59.399 64.784 1.00103.70 S ATOM 12720 SG CYS D 75 82.315 59.400 64.364 1.00107.31 S ATOM 12746 SG CYS D 78 80.340 62.643 64.995 1.00103.78 S Time building chain proxies: 16.27, per 1000 atoms: 0.55 Number of scatterers: 29379 At special positions: 0 Unit cell: (134.2, 162.8, 191.4, 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 99 16.00 P 103 15.00 Mg 1 11.99 O 5841 8.00 N 5245 7.00 C 18088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2000 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 978 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 891 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 968 " pdb="ZN ZN D2000 " - pdb=" SG CYS D 975 " pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 62 " Number of angles added : 12 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6466 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 44 sheets defined 41.8% alpha, 14.7% beta 45 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 10.49 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.211A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.597A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.637A pdb=" N SER B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 224 removed outlier: 4.419A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 removed outlier: 4.310A pdb=" N SER C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 77 removed outlier: 3.753A pdb=" N ARG C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 118 through 125 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.947A pdb=" N LEU C 237 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.989A pdb=" N LYS C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 301 removed outlier: 4.803A pdb=" N LEU C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU C 297 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 380 through 407 removed outlier: 3.662A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 406 " --> pdb=" O GLU C 402 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN C 407 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 444 through 452 removed outlier: 3.645A pdb=" N LYS C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.821A pdb=" N TYR C 480 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 539 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 612 Processing helix chain 'C' and resid 632 through 637 Processing helix chain 'C' and resid 739 through 744 Processing helix chain 'C' and resid 815 through 826 Processing helix chain 'C' and resid 928 through 943 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.607A pdb=" N ALA C 957 " --> pdb=" O ASP C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 991 Processing helix chain 'C' and resid 1036 through 1041 removed outlier: 3.566A pdb=" N LYS C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1069 through 1080 Processing helix chain 'C' and resid 1081 through 1090 Processing helix chain 'C' and resid 1095 through 1109 removed outlier: 4.362A pdb=" N VAL C1100 " --> pdb=" O THR C1096 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS C1101 " --> pdb=" O VAL C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1118 through 1131 removed outlier: 3.812A pdb=" N LYS C1122 " --> pdb=" O PRO C1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.921A pdb=" N VAL D 87 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.887A pdb=" N ILE D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 186 removed outlier: 3.636A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER D 149 " --> pdb=" O HIS D 145 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N THR D 150 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 228 removed outlier: 3.775A pdb=" N VAL D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG D 198 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 286 through 305 removed outlier: 4.319A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.613A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 361 removed outlier: 3.933A pdb=" N LEU D 343 " --> pdb=" O ASP D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 445 through 452 removed outlier: 3.884A pdb=" N GLU D 450 " --> pdb=" O LEU D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 481 through 492 removed outlier: 4.370A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.522A pdb=" N ASN D 564 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 590 removed outlier: 3.741A pdb=" N LEU D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 668 through 675 Processing helix chain 'D' and resid 689 through 704 Processing helix chain 'D' and resid 705 through 726 Processing helix chain 'D' and resid 741 through 762 removed outlier: 3.840A pdb=" N ARG D 752 " --> pdb=" O HIS D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 793 removed outlier: 3.558A pdb=" N ARG D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 805 Processing helix chain 'D' and resid 810 through 818 removed outlier: 3.669A pdb=" N THR D 814 " --> pdb=" O ASN D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 881 removed outlier: 4.049A pdb=" N HIS D 854 " --> pdb=" O PHE D 850 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 956 Processing helix chain 'D' and resid 964 through 968 removed outlier: 3.800A pdb=" N CYS D 968 " --> pdb=" O VAL D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 980 Processing helix chain 'D' and resid 994 through 1005 Processing helix chain 'D' and resid 1027 through 1035 removed outlier: 3.526A pdb=" N VAL D1031 " --> pdb=" O GLY D1027 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU D1033 " --> pdb=" O PRO D1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 1117 through 1125 removed outlier: 3.589A pdb=" N VAL D1121 " --> pdb=" O ASP D1117 " (cutoff:3.500A) Processing helix chain 'D' and resid 1126 through 1144 removed outlier: 3.600A pdb=" N GLN D1131 " --> pdb=" O PRO D1127 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D1141 " --> pdb=" O GLU D1137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D1144 " --> pdb=" O GLU D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1150 through 1153 Processing helix chain 'D' and resid 1154 through 1160 removed outlier: 3.820A pdb=" N GLN D1160 " --> pdb=" O VAL D1156 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1187 Processing helix chain 'D' and resid 1211 through 1216 removed outlier: 3.548A pdb=" N ALA D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) Processing helix chain 'D' and resid 1219 through 1224 Processing helix chain 'D' and resid 1228 through 1237 removed outlier: 3.622A pdb=" N ASP D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1255 Processing helix chain 'D' and resid 1260 through 1263 Processing helix chain 'D' and resid 1264 through 1269 removed outlier: 3.594A pdb=" N ASN D1269 " --> pdb=" O ASN D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1275 through 1281 Processing helix chain 'E' and resid 33 through 37 removed outlier: 3.824A pdb=" N THR E 36 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 37 " --> pdb=" O GLY E 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 33 through 37' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 49 through 70 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'F' and resid 212 through 221 Processing helix chain 'F' and resid 226 through 236 Processing helix chain 'F' and resid 242 through 268 Processing helix chain 'F' and resid 274 through 308 removed outlier: 3.570A pdb=" N TRP F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ARG F 301 " --> pdb=" O GLU F 297 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 334 Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.744A pdb=" N LYS F 339 " --> pdb=" O ASP F 336 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 340 " --> pdb=" O TYR F 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 336 through 340' Processing helix chain 'F' and resid 342 through 363 removed outlier: 3.823A pdb=" N TYR F 346 " --> pdb=" O LYS F 342 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP F 349 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TRP F 350 " --> pdb=" O TYR F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 391 Processing helix chain 'F' and resid 395 through 403 Processing helix chain 'F' and resid 408 through 417 Processing helix chain 'F' and resid 448 through 466 removed outlier: 3.629A pdb=" N THR F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 480 removed outlier: 3.541A pdb=" N VAL F 475 " --> pdb=" O GLU F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 497 Processing helix chain 'F' and resid 499 through 515 Processing helix chain 'F' and resid 516 through 521 Processing helix chain 'F' and resid 523 through 527 removed outlier: 3.639A pdb=" N LEU F 527 " --> pdb=" O ARG F 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 110 Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 84 through 97 Processing helix chain 'M' and resid 100 through 118 Processing helix chain 'M' and resid 121 through 144 Processing helix chain 'M' and resid 148 through 160 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.759A pdb=" N ARG A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS A 191 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 178 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE A 193 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR A 176 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASP A 195 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 174 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU A 197 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.534A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.902A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.731A pdb=" N VAL B 111 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR B 96 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.396A pdb=" N VAL C 39 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.553A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA C 131 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP C 156 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU C 133 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.553A pdb=" N PHE C 134 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 112 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR M 34 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE M 22 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL M 36 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU M 18 " --> pdb=" O LYS M 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 166 through 168 Processing sheet with id=AB6, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.410A pdb=" N SER C 177 " --> pdb=" O SER C 456 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 184 through 185 removed outlier: 3.804A pdb=" N LEU C 212 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 188 through 191 Processing sheet with id=AB9, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AC1, first strand: chain 'C' and resid 505 through 506 removed outlier: 5.018A pdb=" N GLU C 527 " --> pdb=" O LYS C 518 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N VAL C 520 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER C 525 " --> pdb=" O VAL C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 505 through 506 Processing sheet with id=AC3, first strand: chain 'C' and resid 558 through 560 Processing sheet with id=AC4, first strand: chain 'C' and resid 642 through 643 removed outlier: 6.591A pdb=" N VAL C 642 " --> pdb=" O ILE C 702 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 667 through 671 removed outlier: 6.871A pdb=" N TYR C 657 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL C 653 " --> pdb=" O TYR C 657 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR C 659 " --> pdb=" O GLU C 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AC7, first strand: chain 'C' and resid 1007 through 1008 removed outlier: 6.980A pdb=" N ILE C 735 " --> pdb=" O GLY C 896 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ILE C 898 " --> pdb=" O ILE C 735 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 737 " --> pdb=" O ILE C 898 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 736 " --> pdb=" O ILE C 916 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C1026 " --> pdb=" O VAL C 721 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 749 through 760 removed outlier: 3.613A pdb=" N GLU C 867 " --> pdb=" O ALA C 759 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY C 849 " --> pdb=" O TYR C 872 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA C 874 " --> pdb=" O VAL C 847 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N VAL C 847 " --> pdb=" O ALA C 874 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N LYS C 876 " --> pdb=" O GLY C 845 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY C 845 " --> pdb=" O LYS C 876 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 845 " --> pdb=" O VAL C 796 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD1, first strand: chain 'C' and resid 801 through 803 removed outlier: 6.714A pdb=" N LEU C 837 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 944 through 945 Processing sheet with id=AD3, first strand: chain 'C' and resid 1066 through 1068 removed outlier: 3.691A pdb=" N GLN C1066 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.749A pdb=" N GLU D 9 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.492A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.268A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.606A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER D 138 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 328 through 329 Processing sheet with id=AD8, first strand: chain 'D' and resid 425 through 432 removed outlier: 7.414A pdb=" N ALA D 521 " --> pdb=" O PRO D 444 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 632 through 637 Processing sheet with id=AE1, first strand: chain 'D' and resid 886 through 888 Processing sheet with id=AE2, first strand: chain 'D' and resid 897 through 899 removed outlier: 3.808A pdb=" N VAL D 960 " --> pdb=" O VAL D 899 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 929 through 930 removed outlier: 6.924A pdb=" N ALA D 929 " --> pdb=" O ILE D 937 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1075 through 1077 Processing sheet with id=AE5, first strand: chain 'D' and resid 1180 through 1182 removed outlier: 6.588A pdb=" N ALA D1202 " --> pdb=" O ILE D1168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1274 Processing sheet with id=AE7, first strand: chain 'F' and resid 439 through 441 removed outlier: 3.610A pdb=" N GLY J 8 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 39 through 45 1211 hydrogen bonds defined for protein. 3456 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 117 hydrogen bonds 234 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 13.77 Time building geometry restraints manager: 8.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4952 1.31 - 1.43: 7747 1.43 - 1.56: 17000 1.56 - 1.68: 205 1.68 - 1.81: 175 Bond restraints: 30079 Sorted by residual: bond pdb=" C GLY D 442 " pdb=" N LEU D 443 " ideal model delta sigma weight residual 1.332 1.241 0.092 1.44e-02 4.82e+03 4.04e+01 bond pdb=" C ASP C 733 " pdb=" O ASP C 733 " ideal model delta sigma weight residual 1.238 1.179 0.058 1.83e-02 2.99e+03 1.02e+01 bond pdb=" CB THR D1234 " pdb=" CG2 THR D1234 " ideal model delta sigma weight residual 1.521 1.416 0.105 3.30e-02 9.18e+02 1.01e+01 bond pdb=" CB THR D 590 " pdb=" CG2 THR D 590 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.83e+00 bond pdb=" CB MET D 559 " pdb=" CG MET D 559 " ideal model delta sigma weight residual 1.520 1.427 0.093 3.00e-02 1.11e+03 9.67e+00 ... (remaining 30074 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.63: 40699 3.63 - 7.27: 434 7.27 - 10.90: 30 10.90 - 14.53: 6 14.53 - 18.17: 1 Bond angle restraints: 41170 Sorted by residual: angle pdb=" C ARG D 578 " pdb=" N LEU D 579 " pdb=" CA LEU D 579 " ideal model delta sigma weight residual 121.54 135.25 -13.71 1.91e+00 2.74e-01 5.15e+01 angle pdb=" C ASP M 147 " pdb=" N ALA M 148 " pdb=" CA ALA M 148 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CA TYR E 56 " pdb=" CB TYR E 56 " pdb=" CG TYR E 56 " ideal model delta sigma weight residual 113.90 122.08 -8.18 1.80e+00 3.09e-01 2.07e+01 angle pdb=" CA GLU C 962 " pdb=" CB GLU C 962 " pdb=" CG GLU C 962 " ideal model delta sigma weight residual 114.10 122.95 -8.85 2.00e+00 2.50e-01 1.96e+01 angle pdb=" C GLU F 268 " pdb=" N ARG F 269 " pdb=" CA ARG F 269 " ideal model delta sigma weight residual 122.46 128.53 -6.07 1.41e+00 5.03e-01 1.86e+01 ... (remaining 41165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 17176 35.30 - 70.60: 916 70.60 - 105.91: 32 105.91 - 141.21: 0 141.21 - 176.51: 3 Dihedral angle restraints: 18127 sinusoidal: 8076 harmonic: 10051 Sorted by residual: dihedral pdb=" CA GLU C 962 " pdb=" C GLU C 962 " pdb=" N LEU C 963 " pdb=" CA LEU C 963 " ideal model delta harmonic sigma weight residual 180.00 142.06 37.94 0 5.00e+00 4.00e-02 5.76e+01 dihedral pdb=" CA PRO C 774 " pdb=" C PRO C 774 " pdb=" N ASN C 775 " pdb=" CA ASN C 775 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA SER C1093 " pdb=" C SER C1093 " pdb=" N ASP C1094 " pdb=" CA ASP C1094 " ideal model delta harmonic sigma weight residual -180.00 -147.89 -32.11 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 18124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3262 0.067 - 0.134: 1181 0.134 - 0.201: 204 0.201 - 0.268: 34 0.268 - 0.335: 9 Chirality restraints: 4690 Sorted by residual: chirality pdb=" CB VAL C1037 " pdb=" CA VAL C1037 " pdb=" CG1 VAL C1037 " pdb=" CG2 VAL C1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE C 702 " pdb=" CA ILE C 702 " pdb=" CG1 ILE C 702 " pdb=" CG2 ILE C 702 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB ILE D 320 " pdb=" CA ILE D 320 " pdb=" CG1 ILE D 320 " pdb=" CG2 ILE D 320 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 4687 not shown) Planarity restraints: 5057 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 579 " 0.033 2.00e-02 2.50e+03 6.42e-02 4.12e+01 pdb=" C LEU D 579 " -0.111 2.00e-02 2.50e+03 pdb=" O LEU D 579 " 0.041 2.00e-02 2.50e+03 pdb=" N ASP D 580 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA M 148 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ALA M 148 " 0.059 2.00e-02 2.50e+03 pdb=" O ALA M 148 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS M 149 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 444 " -0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 445 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 445 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 445 " -0.045 5.00e-02 4.00e+02 ... (remaining 5054 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 349 2.62 - 3.19: 23199 3.19 - 3.76: 44870 3.76 - 4.33: 61351 4.33 - 4.90: 104782 Nonbonded interactions: 234551 Sorted by model distance: nonbonded pdb=" OD1 ASP D 537 " pdb="MG MG D2002 " model vdw 2.047 2.170 nonbonded pdb=" OD1 ASP D 539 " pdb="MG MG D2002 " model vdw 2.112 2.170 nonbonded pdb=" O SER D 338 " pdb=" OG SER D 338 " model vdw 2.173 3.040 nonbonded pdb=" OE2 GLU C 146 " pdb=" OH TYR M 11 " model vdw 2.237 3.040 nonbonded pdb=" OE2 GLU D 49 " pdb=" OG1 THR D 55 " model vdw 2.241 3.040 ... (remaining 234546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 129 or (resid 130 and (name N or \ name CA or name C or name O or name CB )) or resid 131 through 134 or (resid 135 \ and (name N or name CA or name C or name O or name CB )) or resid 136 through 1 \ 52 or (resid 153 through 154 and (name N or name CA or name C or name O or name \ CB )) or resid 155 through 157 or (resid 158 and (name N or name CA or name C or \ name O or name CB )) or resid 159 through 160 or (resid 161 and (name N or name \ CA or name C or name O or name CB )) or resid 162 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 223 o \ r (resid 224 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 25 through 226)) selection = (chain 'B' and resid 2 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.030 Extract box with map and model: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 77.620 Find NCS groups from input model: 0.560 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.016 0.153 30087 Z= 0.628 Angle : 1.064 18.167 41182 Z= 0.582 Chirality : 0.069 0.335 4690 Planarity : 0.009 0.083 5057 Dihedral : 18.369 176.509 11661 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 7.82 % Allowed : 11.61 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.12), residues: 3489 helix: -1.33 (0.12), residues: 1388 sheet: -1.30 (0.24), residues: 427 loop : -2.03 (0.13), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 944 HIS 0.018 0.002 HIS C1042 PHE 0.033 0.004 PHE C 906 TYR 0.030 0.004 TYR D 586 ARG 0.008 0.001 ARG C 390 Details of bonding type rmsd hydrogen bonds : bond 0.15693 ( 1318) hydrogen bonds : angle 6.23360 ( 3690) metal coordination : bond 0.09588 ( 8) metal coordination : angle 10.41482 ( 12) covalent geometry : bond 0.01564 (30079) covalent geometry : angle 1.04917 (41170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 303 time to evaluate : 3.080 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7961 (ttmm) REVERT: A 91 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: A 224 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6570 (mm-30) REVERT: B 5 GLN cc_start: 0.7220 (tt0) cc_final: 0.6881 (tt0) REVERT: B 20 GLN cc_start: 0.8604 (tt0) cc_final: 0.8317 (tt0) REVERT: B 34 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 126 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7534 (t0) REVERT: C 190 THR cc_start: 0.7862 (OUTLIER) cc_final: 0.7650 (p) REVERT: C 220 ASP cc_start: 0.7973 (t0) cc_final: 0.7636 (t0) REVERT: C 298 ASN cc_start: 0.8112 (m110) cc_final: 0.7500 (m110) REVERT: C 303 GLU cc_start: 0.7695 (mp0) cc_final: 0.7363 (mp0) REVERT: C 305 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7796 (mtm180) REVERT: C 471 GLU cc_start: 0.8116 (tp30) cc_final: 0.7891 (tp30) REVERT: C 551 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7749 (p0) REVERT: C 584 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7938 (ptp-170) REVERT: C 672 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.7489 (mmp) REVERT: C 685 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8298 (m-40) REVERT: C 778 ASP cc_start: 0.8172 (t70) cc_final: 0.7754 (t0) REVERT: C 947 ASP cc_start: 0.7882 (p0) cc_final: 0.7296 (p0) REVERT: D 123 LYS cc_start: 0.7887 (mptp) cc_final: 0.7514 (mmtm) REVERT: D 138 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8025 (p) REVERT: D 415 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7927 (tp-100) REVERT: D 480 ARG cc_start: 0.7855 (mpt90) cc_final: 0.7647 (mpt90) REVERT: D 581 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8826 (mtp) REVERT: D 598 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: D 688 MET cc_start: 0.8796 (mmt) cc_final: 0.8548 (mmt) REVERT: D 950 ASP cc_start: 0.8329 (m-30) cc_final: 0.7980 (m-30) REVERT: D 972 THR cc_start: 0.8355 (p) cc_final: 0.8117 (t) REVERT: D 1041 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7810 (ttm-80) REVERT: D 1115 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7223 (p) REVERT: F 468 SER cc_start: 0.5626 (OUTLIER) cc_final: 0.5286 (p) REVERT: J 7 ARG cc_start: 0.7888 (ttm-80) cc_final: 0.7546 (ttm110) outliers start: 229 outliers final: 118 residues processed: 486 average time/residue: 1.2715 time to fit residues: 738.0449 Evaluate side-chains 404 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 271 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 490 GLU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 534 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 573 SER Chi-restraints excluded: chain C residue 584 ARG Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 672 MET Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 738 SER Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 834 ASP Chi-restraints excluded: chain C residue 836 SER Chi-restraints excluded: chain C residue 844 SER Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 909 ASP Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 934 THR Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1094 ASP Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 576 MET Chi-restraints excluded: chain D residue 581 MET Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 598 GLU Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 971 SER Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1115 SER Chi-restraints excluded: chain D residue 1238 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 21 ASN Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 0.8980 chunk 269 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 279 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 323 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN C 415 GLN C 841 HIS C 941 HIS C1042 HIS E 70 GLN F 485 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.094561 restraints weight = 34854.875| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.45 r_work: 0.2913 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30087 Z= 0.133 Angle : 0.569 12.366 41182 Z= 0.307 Chirality : 0.042 0.170 4690 Planarity : 0.006 0.073 5057 Dihedral : 17.521 179.951 5174 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.30 % Allowed : 15.37 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.13), residues: 3489 helix: 0.35 (0.14), residues: 1377 sheet: -0.68 (0.27), residues: 374 loop : -1.61 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 70 HIS 0.004 0.001 HIS D 767 PHE 0.011 0.001 PHE C 906 TYR 0.011 0.001 TYR D 586 ARG 0.008 0.000 ARG C 225 Details of bonding type rmsd hydrogen bonds : bond 0.04766 ( 1318) hydrogen bonds : angle 4.56310 ( 3690) metal coordination : bond 0.00455 ( 8) metal coordination : angle 2.34451 ( 12) covalent geometry : bond 0.00290 (30079) covalent geometry : angle 0.56765 (41170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 287 time to evaluate : 3.822 Fit side-chains revert: symmetry clash REVERT: A 81 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7350 (tppp) REVERT: A 133 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7802 (ttmm) REVERT: A 224 GLU cc_start: 0.6272 (mm-30) cc_final: 0.5950 (mm-30) REVERT: B 5 GLN cc_start: 0.6888 (tt0) cc_final: 0.6681 (tt0) REVERT: B 20 GLN cc_start: 0.8134 (tt0) cc_final: 0.7904 (tt0) REVERT: C 195 THR cc_start: 0.8494 (m) cc_final: 0.8194 (t) REVERT: C 298 ASN cc_start: 0.7875 (m110) cc_final: 0.7381 (m110) REVERT: C 305 ARG cc_start: 0.8258 (mtm180) cc_final: 0.7934 (mtm180) REVERT: C 645 GLU cc_start: 0.7897 (pt0) cc_final: 0.7388 (pt0) REVERT: C 661 MET cc_start: 0.7846 (ttt) cc_final: 0.7608 (tpp) REVERT: C 724 MET cc_start: 0.8526 (ptm) cc_final: 0.8154 (ptm) REVERT: C 947 ASP cc_start: 0.8017 (p0) cc_final: 0.7354 (p0) REVERT: D 56 ARG cc_start: 0.7104 (mtp85) cc_final: 0.6861 (ptp-110) REVERT: D 238 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6740 (tp30) REVERT: D 733 MET cc_start: 0.7791 (ptm) cc_final: 0.7590 (ptp) REVERT: E 105 GLU cc_start: 0.7677 (pt0) cc_final: 0.7309 (pt0) REVERT: F 263 MET cc_start: 0.6943 (tpp) cc_final: 0.6705 (tpp) REVERT: J 7 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7342 (ttm110) outliers start: 126 outliers final: 70 residues processed: 386 average time/residue: 1.5961 time to fit residues: 737.2241 Evaluate side-chains 349 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 278 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 790 VAL Chi-restraints excluded: chain C residue 815 THR Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1037 VAL Chi-restraints excluded: chain C residue 1046 THR Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 259 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 488 GLU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 629 VAL Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 123 optimal weight: 0.0040 chunk 263 optimal weight: 0.0670 chunk 284 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 386 GLN C 841 HIS C1042 HIS D 852 ASN D 854 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN M 13 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.157193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095982 restraints weight = 35357.399| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.44 r_work: 0.2971 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30087 Z= 0.113 Angle : 0.519 11.932 41182 Z= 0.278 Chirality : 0.041 0.177 4690 Planarity : 0.005 0.072 5057 Dihedral : 16.850 179.342 5050 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.72 % Allowed : 16.36 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3489 helix: 1.14 (0.14), residues: 1383 sheet: -0.57 (0.27), residues: 379 loop : -1.34 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 723 HIS 0.003 0.000 HIS M 13 PHE 0.010 0.001 PHE C 153 TYR 0.010 0.001 TYR C 731 ARG 0.010 0.000 ARG D1085 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 1318) hydrogen bonds : angle 4.13984 ( 3690) metal coordination : bond 0.00221 ( 8) metal coordination : angle 2.01043 ( 12) covalent geometry : bond 0.00248 (30079) covalent geometry : angle 0.51776 (41170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 304 time to evaluate : 3.002 Fit side-chains revert: symmetry clash REVERT: A 133 LYS cc_start: 0.8250 (ttpp) cc_final: 0.7855 (ttmm) REVERT: A 224 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5800 (mm-30) REVERT: B 5 GLN cc_start: 0.6776 (tt0) cc_final: 0.6575 (tt0) REVERT: B 52 THR cc_start: 0.8429 (m) cc_final: 0.8123 (p) REVERT: B 99 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6663 (ttmp) REVERT: C 195 THR cc_start: 0.8568 (m) cc_final: 0.8320 (t) REVERT: C 298 ASN cc_start: 0.7707 (m110) cc_final: 0.7294 (m-40) REVERT: C 302 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.6068 (tttp) REVERT: C 305 ARG cc_start: 0.8421 (mtm180) cc_final: 0.8141 (mtm180) REVERT: C 661 MET cc_start: 0.7912 (ttt) cc_final: 0.7627 (tpp) REVERT: C 724 MET cc_start: 0.8450 (ptm) cc_final: 0.8104 (ptm) REVERT: C 852 VAL cc_start: 0.7924 (OUTLIER) cc_final: 0.7634 (t) REVERT: C 909 ASP cc_start: 0.7848 (t0) cc_final: 0.7555 (m-30) REVERT: C 947 ASP cc_start: 0.8030 (p0) cc_final: 0.7499 (p0) REVERT: D 56 ARG cc_start: 0.7111 (mtp85) cc_final: 0.6853 (ptp-110) REVERT: D 238 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6623 (tp30) REVERT: D 242 ARG cc_start: 0.8195 (tpp-160) cc_final: 0.7896 (tpp80) REVERT: D 911 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7770 (tt) REVERT: D 950 ASP cc_start: 0.8073 (m-30) cc_final: 0.7647 (m-30) REVERT: E 105 GLU cc_start: 0.7569 (pt0) cc_final: 0.7214 (pt0) REVERT: F 266 LEU cc_start: 0.7306 (tp) cc_final: 0.6916 (tt) REVERT: F 277 GLN cc_start: 0.7632 (tp40) cc_final: 0.7401 (mm110) REVERT: J 7 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7306 (ttm110) REVERT: J 106 ARG cc_start: 0.7907 (mmt90) cc_final: 0.7706 (mpt-90) outliers start: 109 outliers final: 54 residues processed: 379 average time/residue: 1.4069 time to fit residues: 629.5669 Evaluate side-chains 344 residues out of total 2961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 285 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 302 LYS Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 373 PHE Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 683 CYS Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 852 VAL Chi-restraints excluded: chain C residue 936 LEU Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 1030 ILE Chi-restraints excluded: chain C residue 1063 PHE Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 262 GLN Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 635 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 885 ILE Chi-restraints excluded: chain D residue 901 LEU Chi-restraints excluded: chain D residue 911 ILE Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 960 VAL Chi-restraints excluded: chain D residue 1206 VAL Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 27 ARG Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain M residue 39 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 57.7245 > 50: distance: 68 - 73: 8.860 distance: 73 - 74: 15.615 distance: 74 - 75: 9.918 distance: 74 - 77: 3.342 distance: 75 - 76: 5.503 distance: 75 - 81: 4.607 distance: 77 - 78: 16.114 distance: 78 - 79: 11.431 distance: 79 - 80: 7.831 distance: 81 - 82: 6.074 distance: 82 - 83: 14.603 distance: 82 - 85: 3.915 distance: 83 - 84: 23.332 distance: 83 - 91: 11.535 distance: 84 - 116: 12.744 distance: 85 - 86: 11.704 distance: 86 - 87: 11.267 distance: 86 - 88: 5.713 distance: 87 - 89: 15.280 distance: 88 - 90: 12.852 distance: 89 - 90: 5.184 distance: 91 - 92: 8.337 distance: 92 - 93: 10.444 distance: 92 - 95: 12.907 distance: 93 - 94: 32.374 distance: 93 - 100: 18.730 distance: 94 - 125: 16.622 distance: 95 - 96: 24.408 distance: 96 - 97: 16.396 distance: 97 - 98: 15.346 distance: 98 - 99: 31.408 distance: 100 - 101: 10.510 distance: 101 - 102: 6.197 distance: 101 - 104: 32.621 distance: 102 - 103: 15.919 distance: 102 - 109: 19.628 distance: 103 - 130: 28.469 distance: 104 - 105: 19.310 distance: 105 - 106: 17.358 distance: 106 - 107: 9.911 distance: 107 - 108: 18.645 distance: 109 - 110: 10.538 distance: 110 - 111: 13.101 distance: 110 - 113: 7.243 distance: 111 - 112: 16.229 distance: 111 - 116: 13.562 distance: 112 - 135: 33.560 distance: 113 - 114: 21.666 distance: 113 - 115: 9.591 distance: 116 - 117: 12.272 distance: 117 - 118: 13.417 distance: 117 - 120: 5.207 distance: 118 - 119: 28.485 distance: 118 - 125: 7.225 distance: 119 - 143: 27.857 distance: 120 - 121: 9.906 distance: 121 - 122: 21.767 distance: 122 - 123: 20.271 distance: 122 - 124: 13.420 distance: 125 - 126: 14.520 distance: 126 - 127: 14.292 distance: 126 - 129: 18.606 distance: 127 - 128: 12.008 distance: 127 - 130: 39.521 distance: 128 - 151: 21.238 distance: 130 - 131: 31.941 distance: 131 - 132: 22.986 distance: 131 - 134: 28.084 distance: 132 - 133: 14.521 distance: 132 - 135: 4.858 distance: 133 - 159: 17.156 distance: 135 - 136: 7.937 distance: 136 - 137: 13.347 distance: 136 - 139: 17.990 distance: 137 - 138: 21.967 distance: 137 - 143: 30.989 distance: 138 - 165: 6.968 distance: 139 - 140: 15.839 distance: 139 - 141: 14.485 distance: 140 - 142: 15.509 distance: 143 - 144: 10.797 distance: 144 - 145: 18.827 distance: 144 - 147: 15.273 distance: 145 - 146: 8.565 distance: 145 - 151: 13.561 distance: 146 - 173: 17.877 distance: 147 - 148: 24.749 distance: 147 - 149: 15.061 distance: 148 - 150: 20.730