Starting phenix.real_space_refine on Sat Mar 7 10:22:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yfp_33796/03_2026/7yfp_33796.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yfp_33796/03_2026/7yfp_33796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yfp_33796/03_2026/7yfp_33796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yfp_33796/03_2026/7yfp_33796.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yfp_33796/03_2026/7yfp_33796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yfp_33796/03_2026/7yfp_33796.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 31 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 168 5.16 5 C 26357 2.51 5 N 6867 2.21 5 O 7554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40949 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3172 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3777 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1668 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 28374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3475, 28374 Classifications: {'peptide': 3475} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'CIS': 3, 'PTRANS': 146, 'TRANS': 3325} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.59, per 1000 atoms: 0.21 Number of scatterers: 40949 At special positions: 0 Unit cell: (138.6, 168.96, 248.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 3 15.00 O 7554 8.00 N 6867 7.00 C 26357 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 3.2 seconds 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9740 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 22 sheets defined 64.7% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 4.186A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 263 Proline residue: A 258 - end of helix removed outlier: 3.585A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.647A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.991A pdb=" N GLY B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 98 removed outlier: 4.464A pdb=" N GLU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 142 through 151 Processing helix chain 'B' and resid 186 through 198 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 254 through 257 removed outlier: 3.670A pdb=" N GLU B 257 " --> pdb=" O THR B 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 257' Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 281 through 294 removed outlier: 4.151A pdb=" N ALA B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 413 through 417 Processing helix chain 'B' and resid 419 through 432 Processing helix chain 'B' and resid 446 through 449 Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 472 through 479 removed outlier: 3.666A pdb=" N GLY B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'D' and resid 25 through 48 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 286 through 297 Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.557A pdb=" N ARG D 305 " --> pdb=" O LEU D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 336 Processing helix chain 'D' and resid 357 through 398 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 638 through 645 removed outlier: 4.902A pdb=" N GLN D 643 " --> pdb=" O ARG D 640 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 644 " --> pdb=" O TYR D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 666 Processing helix chain 'D' and resid 668 through 677 Processing helix chain 'D' and resid 692 through 704 Processing helix chain 'D' and resid 708 through 712 Processing helix chain 'D' and resid 716 through 735 removed outlier: 3.563A pdb=" N ASN D 735 " --> pdb=" O GLN D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 772 removed outlier: 3.653A pdb=" N ARG D 756 " --> pdb=" O HIS D 752 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP D 757 " --> pdb=" O ARG D 753 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU D 762 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS D 766 " --> pdb=" O GLU D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 103 Processing helix chain 'E' and resid 110 through 114 Processing helix chain 'E' and resid 165 through 177 removed outlier: 4.191A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 177 " --> pdb=" O PHE E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 removed outlier: 4.310A pdb=" N ASP E 188 " --> pdb=" O PHE E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 217 Processing helix chain 'E' and resid 220 through 226 removed outlier: 3.882A pdb=" N SER E 224 " --> pdb=" O ASN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 246 Processing helix chain 'E' and resid 247 through 266 Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 281 through 284 Processing helix chain 'E' and resid 299 through 308 Processing helix chain 'F' and resid 521 through 535 removed outlier: 4.093A pdb=" N GLU F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 579 removed outlier: 4.367A pdb=" N TYR F 577 " --> pdb=" O ARG F 574 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER F 579 " --> pdb=" O PHE F 576 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.557A pdb=" N ILE T 7 " --> pdb=" O LEU T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 14 No H-bonds generated for 'chain 'T' and resid 12 through 14' Processing helix chain 'T' and resid 22 through 27 Processing helix chain 'T' and resid 28 through 34 removed outlier: 4.101A pdb=" N ILE T 34 " --> pdb=" O GLU T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 47 through 61 Proline residue: T 53 - end of helix Processing helix chain 'T' and resid 72 through 85 Processing helix chain 'T' and resid 92 through 107 removed outlier: 4.868A pdb=" N LEU T 100 " --> pdb=" O ALA T 96 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU T 101 " --> pdb=" O MET T 97 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE T 102 " --> pdb=" O GLU T 98 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL T 106 " --> pdb=" O PHE T 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 131 removed outlier: 4.492A pdb=" N SER T 131 " --> pdb=" O LYS T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 137 through 158 removed outlier: 4.023A pdb=" N ARG T 142 " --> pdb=" O ASP T 138 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE T 143 " --> pdb=" O SER T 139 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE T 144 " --> pdb=" O PHE T 140 " (cutoff:3.500A) Proline residue: T 152 - end of helix Processing helix chain 'T' and resid 218 through 223 removed outlier: 4.146A pdb=" N LYS T 222 " --> pdb=" O MET T 218 " (cutoff:3.500A) Processing helix chain 'T' and resid 231 through 244 removed outlier: 4.731A pdb=" N SER T 237 " --> pdb=" O THR T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 258 Processing helix chain 'T' and resid 291 through 314 removed outlier: 4.427A pdb=" N ILE T 295 " --> pdb=" O TYR T 291 " (cutoff:3.500A) Processing helix chain 'T' and resid 323 through 335 removed outlier: 4.552A pdb=" N ASP T 327 " --> pdb=" O ASN T 323 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP T 335 " --> pdb=" O ARG T 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 357 removed outlier: 3.831A pdb=" N GLU T 346 " --> pdb=" O SER T 342 " (cutoff:3.500A) Processing helix chain 'T' and resid 358 through 362 Processing helix chain 'T' and resid 363 through 369 Processing helix chain 'T' and resid 374 through 378 Processing helix chain 'T' and resid 380 through 403 removed outlier: 4.993A pdb=" N THR T 386 " --> pdb=" O THR T 382 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU T 387 " --> pdb=" O MET T 383 " (cutoff:3.500A) Proline residue: T 389 - end of helix removed outlier: 4.175A pdb=" N ARG T 403 " --> pdb=" O ILE T 399 " (cutoff:3.500A) Processing helix chain 'T' and resid 407 through 424 Processing helix chain 'T' and resid 429 through 453 removed outlier: 4.078A pdb=" N GLU T 444 " --> pdb=" O LEU T 440 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG T 445 " --> pdb=" O ASN T 441 " (cutoff:3.500A) Processing helix chain 'T' and resid 456 through 504 removed outlier: 3.958A pdb=" N LEU T 478 " --> pdb=" O ARG T 474 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASP T 483 " --> pdb=" O ASN T 479 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N THR T 484 " --> pdb=" O ARG T 480 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS T 487 " --> pdb=" O ASP T 483 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR T 488 " --> pdb=" O THR T 484 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR T 494 " --> pdb=" O GLY T 490 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS T 502 " --> pdb=" O GLU T 498 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU T 503 " --> pdb=" O LYS T 499 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 Processing helix chain 'T' and resid 562 through 567 Processing helix chain 'T' and resid 578 through 601 Processing helix chain 'T' and resid 602 through 604 No H-bonds generated for 'chain 'T' and resid 602 through 604' Processing helix chain 'T' and resid 607 through 612 removed outlier: 4.149A pdb=" N TYR T 611 " --> pdb=" O PRO T 607 " (cutoff:3.500A) Processing helix chain 'T' and resid 627 through 645 Processing helix chain 'T' and resid 646 through 648 No H-bonds generated for 'chain 'T' and resid 646 through 648' Processing helix chain 'T' and resid 677 through 691 Processing helix chain 'T' and resid 694 through 714 removed outlier: 4.160A pdb=" N GLN T 704 " --> pdb=" O GLU T 700 " (cutoff:3.500A) Proline residue: T 707 - end of helix Processing helix chain 'T' and resid 717 through 729 removed outlier: 3.764A pdb=" N HIS T 721 " --> pdb=" O SER T 717 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER T 729 " --> pdb=" O SER T 725 " (cutoff:3.500A) Processing helix chain 'T' and resid 732 through 748 Processing helix chain 'T' and resid 749 through 751 No H-bonds generated for 'chain 'T' and resid 749 through 751' Processing helix chain 'T' and resid 755 through 776 Processing helix chain 'T' and resid 787 through 802 removed outlier: 3.592A pdb=" N THR T 801 " --> pdb=" O LYS T 797 " (cutoff:3.500A) Processing helix chain 'T' and resid 804 through 819 removed outlier: 4.303A pdb=" N TYR T 808 " --> pdb=" O GLU T 804 " (cutoff:3.500A) Processing helix chain 'T' and resid 831 through 844 removed outlier: 3.801A pdb=" N LEU T 835 " --> pdb=" O ILE T 831 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN T 844 " --> pdb=" O GLN T 840 " (cutoff:3.500A) Processing helix chain 'T' and resid 855 through 864 Processing helix chain 'T' and resid 879 through 889 Processing helix chain 'T' and resid 893 through 905 removed outlier: 3.662A pdb=" N ILE T 905 " --> pdb=" O LEU T 901 " (cutoff:3.500A) Processing helix chain 'T' and resid 912 through 918 removed outlier: 4.196A pdb=" N ILE T 916 " --> pdb=" O TYR T 912 " (cutoff:3.500A) Processing helix chain 'T' and resid 920 through 932 Processing helix chain 'T' and resid 938 through 952 removed outlier: 3.616A pdb=" N LEU T 952 " --> pdb=" O ILE T 948 " (cutoff:3.500A) Processing helix chain 'T' and resid 970 through 974 Processing helix chain 'T' and resid 996 through 1006 Processing helix chain 'T' and resid 1010 through 1034 removed outlier: 4.616A pdb=" N SER T1031 " --> pdb=" O LEU T1027 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER T1032 " --> pdb=" O MET T1028 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU T1034 " --> pdb=" O LYS T1030 " (cutoff:3.500A) Processing helix chain 'T' and resid 1038 through 1052 removed outlier: 3.673A pdb=" N LYS T1044 " --> pdb=" O THR T1040 " (cutoff:3.500A) Processing helix chain 'T' and resid 1068 through 1091 removed outlier: 4.027A pdb=" N SER T1091 " --> pdb=" O PHE T1087 " (cutoff:3.500A) Processing helix chain 'T' and resid 1095 through 1125 Processing helix chain 'T' and resid 1143 through 1155 Proline residue: T1150 - end of helix Processing helix chain 'T' and resid 1157 through 1180 Processing helix chain 'T' and resid 1181 through 1188 Processing helix chain 'T' and resid 1189 through 1203 Processing helix chain 'T' and resid 1205 through 1224 Processing helix chain 'T' and resid 1227 through 1248 removed outlier: 6.427A pdb=" N TYR T1235 " --> pdb=" O LYS T1231 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN T1236 " --> pdb=" O LYS T1232 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU T1237 " --> pdb=" O TYR T1233 " (cutoff:3.500A) Processing helix chain 'T' and resid 1253 through 1273 removed outlier: 4.473A pdb=" N THR T1257 " --> pdb=" O PRO T1253 " (cutoff:3.500A) Processing helix chain 'T' and resid 1283 through 1296 Processing helix chain 'T' and resid 1300 through 1317 Processing helix chain 'T' and resid 1321 through 1326 Processing helix chain 'T' and resid 1329 through 1340 Proline residue: T1336 - end of helix removed outlier: 4.606A pdb=" N LYS T1340 " --> pdb=" O PRO T1336 " (cutoff:3.500A) Processing helix chain 'T' and resid 1346 through 1363 Processing helix chain 'T' and resid 1371 through 1384 Processing helix chain 'T' and resid 1403 through 1425 Processing helix chain 'T' and resid 1436 through 1450 Processing helix chain 'T' and resid 1452 through 1467 Processing helix chain 'T' and resid 1477 through 1490 Proline residue: T1484 - end of helix Processing helix chain 'T' and resid 1496 through 1509 removed outlier: 3.576A pdb=" N GLU T1508 " --> pdb=" O SER T1504 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LEU T1509 " --> pdb=" O LYS T1505 " (cutoff:3.500A) Processing helix chain 'T' and resid 1517 through 1530 removed outlier: 3.724A pdb=" N LYS T1521 " --> pdb=" O GLU T1517 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP T1524 " --> pdb=" O ARG T1520 " (cutoff:3.500A) Processing helix chain 'T' and resid 1531 through 1539 Processing helix chain 'T' and resid 1542 through 1545 Processing helix chain 'T' and resid 1546 through 1562 removed outlier: 3.590A pdb=" N ILE T1558 " --> pdb=" O SER T1554 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE T1559 " --> pdb=" O ILE T1555 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS T1560 " --> pdb=" O ILE T1556 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU T1561 " --> pdb=" O ASN T1557 " (cutoff:3.500A) Processing helix chain 'T' and resid 1568 through 1585 Processing helix chain 'T' and resid 1592 through 1604 removed outlier: 3.971A pdb=" N PHE T1603 " --> pdb=" O TYR T1599 " (cutoff:3.500A) Processing helix chain 'T' and resid 1605 through 1614 Processing helix chain 'T' and resid 1617 through 1630 Processing helix chain 'T' and resid 1634 through 1659 removed outlier: 4.570A pdb=" N ASP T1645 " --> pdb=" O GLU T1641 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASN T1646 " --> pdb=" O LYS T1642 " (cutoff:3.500A) Proline residue: T1656 - end of helix Processing helix chain 'T' and resid 1661 through 1680 Processing helix chain 'T' and resid 1689 through 1709 Processing helix chain 'T' and resid 1715 through 1736 Processing helix chain 'T' and resid 1739 through 1750 removed outlier: 3.714A pdb=" N LEU T1743 " --> pdb=" O ASP T1739 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU T1744 " --> pdb=" O GLN T1740 " (cutoff:3.500A) Processing helix chain 'T' and resid 1761 through 1769 Processing helix chain 'T' and resid 1777 through 1792 removed outlier: 3.680A pdb=" N ASN T1781 " --> pdb=" O GLU T1777 " (cutoff:3.500A) Processing helix chain 'T' and resid 1796 through 1818 Processing helix chain 'T' and resid 1832 through 1844 removed outlier: 3.907A pdb=" N LEU T1836 " --> pdb=" O LYS T1832 " (cutoff:3.500A) Processing helix chain 'T' and resid 1858 through 1875 removed outlier: 3.768A pdb=" N LEU T1865 " --> pdb=" O ARG T1861 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE T1871 " --> pdb=" O LEU T1867 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE T1872 " --> pdb=" O SER T1868 " (cutoff:3.500A) Processing helix chain 'T' and resid 1879 through 1892 Processing helix chain 'T' and resid 1893 through 1896 Processing helix chain 'T' and resid 1898 through 1916 Processing helix chain 'T' and resid 1919 through 1932 removed outlier: 3.501A pdb=" N GLN T1925 " --> pdb=" O LYS T1921 " (cutoff:3.500A) Processing helix chain 'T' and resid 1938 through 1957 Proline residue: T1951 - end of helix Processing helix chain 'T' and resid 1964 through 1976 Processing helix chain 'T' and resid 1980 through 1992 removed outlier: 3.513A pdb=" N ILE T1984 " --> pdb=" O SER T1980 " (cutoff:3.500A) Processing helix chain 'T' and resid 2001 through 2016 removed outlier: 3.828A pdb=" N ASN T2012 " --> pdb=" O ILE T2008 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS T2013 " --> pdb=" O HIS T2009 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE T2016 " --> pdb=" O ASN T2012 " (cutoff:3.500A) Processing helix chain 'T' and resid 2023 through 2043 Processing helix chain 'T' and resid 2090 through 2107 Processing helix chain 'T' and resid 2116 through 2129 removed outlier: 3.598A pdb=" N GLU T2126 " --> pdb=" O ASN T2122 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU T2127 " --> pdb=" O ILE T2123 " (cutoff:3.500A) Processing helix chain 'T' and resid 2140 through 2146 removed outlier: 4.183A pdb=" N GLU T2144 " --> pdb=" O LEU T2140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T2145 " --> pdb=" O VAL T2141 " (cutoff:3.500A) Processing helix chain 'T' and resid 2155 through 2174 removed outlier: 3.528A pdb=" N TYR T2169 " --> pdb=" O LEU T2165 " (cutoff:3.500A) Processing helix chain 'T' and resid 2183 through 2201 removed outlier: 4.375A pdb=" N LYS T2193 " --> pdb=" O ASN T2189 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS T2194 " --> pdb=" O LEU T2190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP T2198 " --> pdb=" O CYS T2194 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N HIS T2199 " --> pdb=" O ILE T2195 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS T2200 " --> pdb=" O LYS T2196 " (cutoff:3.500A) Processing helix chain 'T' and resid 2203 through 2218 removed outlier: 3.597A pdb=" N GLN T2211 " --> pdb=" O GLN T2207 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL T2212 " --> pdb=" O LYS T2208 " (cutoff:3.500A) Processing helix chain 'T' and resid 2221 through 2226 Processing helix chain 'T' and resid 2229 through 2246 Processing helix chain 'T' and resid 2249 through 2267 removed outlier: 3.526A pdb=" N LEU T2263 " --> pdb=" O LEU T2259 " (cutoff:3.500A) Processing helix chain 'T' and resid 2274 through 2294 removed outlier: 3.950A pdb=" N GLN T2294 " --> pdb=" O LEU T2290 " (cutoff:3.500A) Processing helix chain 'T' and resid 2301 through 2322 Processing helix chain 'T' and resid 2328 through 2342 Processing helix chain 'T' and resid 2345 through 2361 removed outlier: 4.519A pdb=" N SER T2358 " --> pdb=" O ASN T2354 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP T2359 " --> pdb=" O MET T2355 " (cutoff:3.500A) Processing helix chain 'T' and resid 2368 through 2379 Processing helix chain 'T' and resid 2381 through 2386 Processing helix chain 'T' and resid 2387 through 2405 Processing helix chain 'T' and resid 2413 through 2423 Proline residue: T2419 - end of helix removed outlier: 4.451A pdb=" N VAL T2422 " --> pdb=" O GLN T2418 " (cutoff:3.500A) Processing helix chain 'T' and resid 2428 through 2442 removed outlier: 3.689A pdb=" N ARG T2434 " --> pdb=" O GLY T2430 " (cutoff:3.500A) Processing helix chain 'T' and resid 2446 through 2457 Processing helix chain 'T' and resid 2469 through 2478 Processing helix chain 'T' and resid 2496 through 2501 Processing helix chain 'T' and resid 2518 through 2535 removed outlier: 4.032A pdb=" N ARG T2535 " --> pdb=" O GLN T2531 " (cutoff:3.500A) Processing helix chain 'T' and resid 2537 through 2550 removed outlier: 4.189A pdb=" N ASP T2543 " --> pdb=" O SER T2539 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE T2548 " --> pdb=" O SER T2544 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) Processing helix chain 'T' and resid 2552 through 2570 removed outlier: 3.894A pdb=" N ILE T2556 " --> pdb=" O ASP T2552 " (cutoff:3.500A) Proline residue: T2565 - end of helix removed outlier: 3.980A pdb=" N SER T2570 " --> pdb=" O GLN T2566 " (cutoff:3.500A) Processing helix chain 'T' and resid 2575 through 2588 removed outlier: 3.801A pdb=" N THR T2585 " --> pdb=" O ARG T2581 " (cutoff:3.500A) Processing helix chain 'T' and resid 2602 through 2612 removed outlier: 4.270A pdb=" N LEU T2606 " --> pdb=" O VAL T2602 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS T2612 " --> pdb=" O ASP T2608 " (cutoff:3.500A) Processing helix chain 'T' and resid 2632 through 2646 removed outlier: 3.897A pdb=" N ILE T2639 " --> pdb=" O GLN T2635 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN T2644 " --> pdb=" O LEU T2640 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER T2645 " --> pdb=" O GLU T2641 " (cutoff:3.500A) Processing helix chain 'T' and resid 2652 through 2670 Processing helix chain 'T' and resid 2671 through 2683 removed outlier: 4.822A pdb=" N GLY T2677 " --> pdb=" O ASP T2673 " (cutoff:3.500A) Processing helix chain 'T' and resid 2685 through 2698 removed outlier: 4.032A pdb=" N ASN T2689 " --> pdb=" O TYR T2685 " (cutoff:3.500A) Processing helix chain 'T' and resid 2699 through 2714 Processing helix chain 'T' and resid 2724 through 2741 Processing helix chain 'T' and resid 2745 through 2751 removed outlier: 3.868A pdb=" N LEU T2749 " --> pdb=" O VAL T2745 " (cutoff:3.500A) Processing helix chain 'T' and resid 2754 through 2761 Processing helix chain 'T' and resid 2772 through 2783 Processing helix chain 'T' and resid 2788 through 2806 removed outlier: 4.165A pdb=" N PHE T2794 " --> pdb=" O ARG T2790 " (cutoff:3.500A) Processing helix chain 'T' and resid 2812 through 2830 removed outlier: 4.094A pdb=" N ASP T2818 " --> pdb=" O ARG T2814 " (cutoff:3.500A) Processing helix chain 'T' and resid 2838 through 2865 removed outlier: 3.877A pdb=" N LEU T2842 " --> pdb=" O ALA T2838 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN T2847 " --> pdb=" O LEU T2843 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR T2865 " --> pdb=" O ASN T2861 " (cutoff:3.500A) Processing helix chain 'T' and resid 2873 through 2887 removed outlier: 4.078A pdb=" N ILE T2877 " --> pdb=" O LYS T2873 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA T2883 " --> pdb=" O ARG T2879 " (cutoff:3.500A) Processing helix chain 'T' and resid 2895 through 2917 removed outlier: 4.776A pdb=" N ALA T2908 " --> pdb=" O TRP T2904 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE T2909 " --> pdb=" O ARG T2905 " (cutoff:3.500A) Processing helix chain 'T' and resid 2918 through 2920 No H-bonds generated for 'chain 'T' and resid 2918 through 2920' Processing helix chain 'T' and resid 2941 through 2958 removed outlier: 4.181A pdb=" N TRP T2945 " --> pdb=" O HIS T2941 " (cutoff:3.500A) Processing helix chain 'T' and resid 2959 through 2967 removed outlier: 4.213A pdb=" N CYS T2963 " --> pdb=" O MET T2959 " (cutoff:3.500A) Processing helix chain 'T' and resid 2968 through 2972 Processing helix chain 'T' and resid 2979 through 2993 Processing helix chain 'T' and resid 2998 through 3003 removed outlier: 4.093A pdb=" N GLY T3002 " --> pdb=" O GLU T2998 " (cutoff:3.500A) Processing helix chain 'T' and resid 3016 through 3033 removed outlier: 3.897A pdb=" N ALA T3020 " --> pdb=" O THR T3016 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU T3021 " --> pdb=" O VAL T3017 " (cutoff:3.500A) Processing helix chain 'T' and resid 3036 through 3051 removed outlier: 4.060A pdb=" N ASP T3050 " --> pdb=" O ALA T3046 " (cutoff:3.500A) Processing helix chain 'T' and resid 3054 through 3071 removed outlier: 3.541A pdb=" N GLN T3059 " --> pdb=" O LYS T3055 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN T3064 " --> pdb=" O TRP T3060 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU T3071 " --> pdb=" O ARG T3067 " (cutoff:3.500A) Processing helix chain 'T' and resid 3078 through 3092 removed outlier: 4.172A pdb=" N LEU T3086 " --> pdb=" O ILE T3082 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN T3087 " --> pdb=" O SER T3083 " (cutoff:3.500A) Processing helix chain 'T' and resid 3097 through 3109 Processing helix chain 'T' and resid 3115 through 3122 Processing helix chain 'T' and resid 3129 through 3134 removed outlier: 3.599A pdb=" N TRP T3133 " --> pdb=" O PRO T3129 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE T3134 " --> pdb=" O VAL T3130 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3129 through 3134' Processing helix chain 'T' and resid 3136 through 3146 Processing helix chain 'T' and resid 3152 through 3163 removed outlier: 3.926A pdb=" N ARG T3158 " --> pdb=" O HIS T3154 " (cutoff:3.500A) Processing helix chain 'T' and resid 3164 through 3182 removed outlier: 4.420A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) Processing helix chain 'T' and resid 3203 through 3218 removed outlier: 3.747A pdb=" N TYR T3207 " --> pdb=" O GLN T3203 " (cutoff:3.500A) Processing helix chain 'T' and resid 3219 through 3236 removed outlier: 3.671A pdb=" N ALA T3231 " --> pdb=" O GLU T3227 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN T3232 " --> pdb=" O SER T3228 " (cutoff:3.500A) Processing helix chain 'T' and resid 3240 through 3263 removed outlier: 4.487A pdb=" N LEU T3263 " --> pdb=" O ASN T3259 " (cutoff:3.500A) Processing helix chain 'T' and resid 3273 through 3283 Processing helix chain 'T' and resid 3288 through 3301 removed outlier: 3.635A pdb=" N ILE T3292 " --> pdb=" O LEU T3288 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG T3293 " --> pdb=" O ALA T3289 " (cutoff:3.500A) Proline residue: T3294 - end of helix Processing helix chain 'T' and resid 3308 through 3328 removed outlier: 3.525A pdb=" N ALA T3328 " --> pdb=" O LYS T3324 " (cutoff:3.500A) Processing helix chain 'T' and resid 3333 through 3338 Processing helix chain 'T' and resid 3338 through 3343 Processing helix chain 'T' and resid 3344 through 3347 Processing helix chain 'T' and resid 3356 through 3360 removed outlier: 3.960A pdb=" N LEU T3360 " --> pdb=" O GLN T3357 " (cutoff:3.500A) Processing helix chain 'T' and resid 3412 through 3433 removed outlier: 4.409A pdb=" N ASN T3427 " --> pdb=" O TYR T3423 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS T3428 " --> pdb=" O ARG T3424 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER T3429 " --> pdb=" O LEU T3425 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN T3433 " --> pdb=" O SER T3429 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3478 Processing helix chain 'T' and resid 3481 through 3498 removed outlier: 4.045A pdb=" N ILE T3485 " --> pdb=" O ASP T3481 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP T3498 " --> pdb=" O ASN T3494 " (cutoff:3.500A) Processing helix chain 'T' and resid 3506 through 3521 removed outlier: 3.655A pdb=" N THR T3519 " --> pdb=" O ASN T3515 " (cutoff:3.500A) Processing helix chain 'T' and resid 3525 through 3535 Processing helix chain 'T' and resid 3540 through 3561 removed outlier: 3.987A pdb=" N SER T3550 " --> pdb=" O LYS T3546 " (cutoff:3.500A) Processing helix chain 'T' and resid 3625 through 3632 Processing helix chain 'T' and resid 3633 through 3640 Processing helix chain 'T' and resid 3640 through 3654 removed outlier: 4.572A pdb=" N PHE T3646 " --> pdb=" O ALA T3642 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU T3654 " --> pdb=" O ARG T3650 " (cutoff:3.500A) Processing helix chain 'T' and resid 3658 through 3678 removed outlier: 3.547A pdb=" N TYR T3662 " --> pdb=" O GLU T3658 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA T3664 " --> pdb=" O ASN T3660 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG T3668 " --> pdb=" O ALA T3664 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP T3669 " --> pdb=" O LEU T3665 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) Processing helix chain 'T' and resid 3685 through 3705 removed outlier: 3.766A pdb=" N ARG T3689 " --> pdb=" O ASN T3685 " (cutoff:3.500A) Processing helix chain 'T' and resid 3717 through 3729 Processing helix chain 'T' and resid 3729 through 3735 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 6.591A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.527A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.546A pdb=" N GLU A 72 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AA6, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA7, first strand: chain 'A' and resid 238 through 242 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.715A pdb=" N VAL B 470 " --> pdb=" O CYS B 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 43 through 47 Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 175 removed outlier: 6.112A pdb=" N LEU B 156 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 411 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VAL B 158 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 408 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB4, first strand: chain 'F' and resid 585 through 587 Processing sheet with id=AB5, first strand: chain 'D' and resid 280 through 282 Processing sheet with id=AB6, first strand: chain 'D' and resid 649 through 650 Processing sheet with id=AB7, first strand: chain 'E' and resid 91 through 96 removed outlier: 4.038A pdb=" N LYS E 107 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 546 through 547 Processing sheet with id=AB9, first strand: chain 'F' and resid 636 through 642 removed outlier: 3.900A pdb=" N ARG F 639 " --> pdb=" O ASP F 651 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 977 through 980 Processing sheet with id=AC2, first strand: chain 'T' and resid 3331 through 3332 removed outlier: 7.517A pdb=" N MET T3392 " --> pdb=" O PHE T3374 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE T3374 " --> pdb=" O MET T3392 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG T3394 " --> pdb=" O ALA T3372 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 3331 through 3332 removed outlier: 4.235A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET T3458 " --> pdb=" O ALA T3404 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 3464 through 3466 2238 hydrogen bonds defined for protein. 6546 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.95 Time building geometry restraints manager: 4.60 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: 9983 1.33 - 1.45: 8290 1.45 - 1.58: 23285 1.58 - 1.70: 5 1.70 - 1.82: 282 Bond restraints: 41845 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.41e+01 bond pdb=" C4 ATP B 501 " pdb=" N9 ATP B 501 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.49e+01 bond pdb=" C5 ATP B 501 " pdb=" N7 ATP B 501 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.08e+01 bond pdb=" C8 ATP B 501 " pdb=" N7 ATP B 501 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.81e+01 ... (remaining 41840 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 56367 4.03 - 8.05: 284 8.05 - 12.08: 11 12.08 - 16.10: 0 16.10 - 20.13: 2 Bond angle restraints: 56664 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 117.03 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" C5 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N3 ATP B 501 " ideal model delta sigma weight residual 126.80 118.93 7.87 1.00e+00 1.00e+00 6.20e+01 angle pdb=" N3 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N9 ATP B 501 " ideal model delta sigma weight residual 127.04 135.00 -7.96 1.15e+00 7.59e-01 4.80e+01 angle pdb=" N PRO T3592 " pdb=" CA PRO T3592 " pdb=" CB PRO T3592 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.42e+01 ... (remaining 56659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 22748 17.99 - 35.98: 2308 35.98 - 53.97: 302 53.97 - 71.96: 59 71.96 - 89.94: 33 Dihedral angle restraints: 25450 sinusoidal: 10517 harmonic: 14933 Sorted by residual: dihedral pdb=" CA ALA D 540 " pdb=" C ALA D 540 " pdb=" N PRO D 541 " pdb=" CA PRO D 541 " ideal model delta harmonic sigma weight residual -180.00 -138.68 -41.32 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA SER D 535 " pdb=" C SER D 535 " pdb=" N LYS D 536 " pdb=" CA LYS D 536 " ideal model delta harmonic sigma weight residual 180.00 141.89 38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" CA THR T1366 " pdb=" C THR T1366 " pdb=" N PHE T1367 " pdb=" CA PHE T1367 " ideal model delta harmonic sigma weight residual 180.00 143.08 36.92 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 25447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5597 0.092 - 0.184: 688 0.184 - 0.276: 104 0.276 - 0.368: 5 0.368 - 0.460: 2 Chirality restraints: 6396 Sorted by residual: chirality pdb=" CA PHE T1988 " pdb=" N PHE T1988 " pdb=" C PHE T1988 " pdb=" CB PHE T1988 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ASN T1557 " pdb=" N ASN T1557 " pdb=" C ASN T1557 " pdb=" CB ASN T1557 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA TYR T1851 " pdb=" N TYR T1851 " pdb=" C TYR T1851 " pdb=" CB TYR T1851 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 6393 not shown) Planarity restraints: 7199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN T1958 " -0.014 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C ASN T1958 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN T1958 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA T1959 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU T1796 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.14e+00 pdb=" C LEU T1796 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU T1796 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP T1797 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU T2719 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO T2720 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO T2720 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO T2720 " -0.039 5.00e-02 4.00e+02 ... (remaining 7196 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 234 2.36 - 3.00: 25958 3.00 - 3.63: 67042 3.63 - 4.27: 92236 4.27 - 4.90: 146132 Nonbonded interactions: 331602 Sorted by model distance: nonbonded pdb=" OD2 ASP T 694 " pdb=" NH2 ARG T1585 " model vdw 1.729 3.120 nonbonded pdb=" CD1 LEU T2320 " pdb=" CB MET T2355 " model vdw 1.855 3.860 nonbonded pdb=" CB ARG T 480 " pdb=" CZ TYR T1760 " model vdw 1.860 3.660 nonbonded pdb=" OD1 ASP T 694 " pdb=" NH2 ARG T1585 " model vdw 1.913 3.120 nonbonded pdb=" CB ARG T 480 " pdb=" OH TYR T1760 " model vdw 1.964 3.440 ... (remaining 331597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 38.350 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.007 0.132 41847 Z= 0.446 Angle : 0.932 20.129 56664 Z= 0.630 Chirality : 0.062 0.460 6396 Planarity : 0.005 0.071 7199 Dihedral : 14.318 89.944 15710 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 27.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.31 % Favored : 88.47 % Rotamer: Outliers : 1.60 % Allowed : 9.60 % Favored : 88.80 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.11), residues: 4978 helix: -0.79 (0.09), residues: 2950 sheet: -3.12 (0.31), residues: 175 loop : -3.91 (0.12), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 13 TYR 0.020 0.002 TYR F 584 PHE 0.029 0.002 PHE T 10 TRP 0.043 0.002 TRP B 469 HIS 0.008 0.001 HIS T2592 Details of bonding type rmsd covalent geometry : bond 0.00667 (41845) covalent geometry : angle 0.93202 (56664) hydrogen bonds : bond 0.12980 ( 2230) hydrogen bonds : angle 5.60882 ( 6546) Misc. bond : bond 0.09322 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 686 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7428 (t0) cc_final: 0.6710 (t0) REVERT: A 190 MET cc_start: 0.9544 (ttm) cc_final: 0.9183 (tmm) REVERT: A 313 MET cc_start: 0.9223 (tpp) cc_final: 0.8827 (mmp) REVERT: A 361 GLU cc_start: 0.9442 (tp30) cc_final: 0.9168 (tp30) REVERT: B 98 LEU cc_start: 0.9621 (mt) cc_final: 0.9231 (mt) REVERT: D 285 LEU cc_start: 0.9201 (mt) cc_final: 0.8738 (tt) REVERT: D 287 LEU cc_start: 0.9416 (tp) cc_final: 0.9215 (tt) REVERT: D 573 ARG cc_start: 0.8802 (ptt180) cc_final: 0.8487 (ptm-80) REVERT: D 609 GLU cc_start: 0.9094 (tp30) cc_final: 0.8542 (tm-30) REVERT: D 656 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8758 (tm-30) REVERT: D 682 TYR cc_start: 0.9085 (t80) cc_final: 0.8780 (t80) REVERT: D 689 GLU cc_start: 0.8556 (tp30) cc_final: 0.8323 (tp30) REVERT: E 223 LEU cc_start: 0.8701 (mt) cc_final: 0.8240 (mp) REVERT: F 525 GLU cc_start: 0.9194 (mp0) cc_final: 0.8992 (mp0) REVERT: F 586 LYS cc_start: 0.8248 (mppt) cc_final: 0.7728 (mmtm) REVERT: F 621 ASP cc_start: 0.9144 (t0) cc_final: 0.8144 (t0) REVERT: T 83 PHE cc_start: 0.8407 (m-80) cc_final: 0.8044 (m-80) REVERT: T 304 PHE cc_start: 0.8507 (m-10) cc_final: 0.8245 (m-80) REVERT: T 307 TYR cc_start: 0.8427 (m-10) cc_final: 0.7976 (m-80) REVERT: T 432 GLN cc_start: 0.8793 (mt0) cc_final: 0.8555 (mt0) REVERT: T 691 MET cc_start: 0.9195 (mmm) cc_final: 0.8750 (mmm) REVERT: T 711 GLU cc_start: 0.9765 (tp30) cc_final: 0.9457 (tp30) REVERT: T 749 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8696 (tppt) REVERT: T 771 MET cc_start: 0.8551 (mmt) cc_final: 0.8273 (mmt) REVERT: T 775 LEU cc_start: 0.8951 (pp) cc_final: 0.8699 (pp) REVERT: T 840 GLN cc_start: 0.8446 (pt0) cc_final: 0.8103 (tm-30) REVERT: T 845 MET cc_start: 0.8639 (ttm) cc_final: 0.8351 (ttp) REVERT: T 965 ASP cc_start: 0.8969 (p0) cc_final: 0.8748 (p0) REVERT: T 1084 GLU cc_start: 0.8656 (pp20) cc_final: 0.8399 (pp20) REVERT: T 1147 ASP cc_start: 0.8995 (t0) cc_final: 0.8625 (t70) REVERT: T 1242 LEU cc_start: 0.9578 (mt) cc_final: 0.9357 (mt) REVERT: T 1246 LYS cc_start: 0.9637 (mtmt) cc_final: 0.9390 (mtpp) REVERT: T 1266 ASP cc_start: 0.9493 (m-30) cc_final: 0.9270 (m-30) REVERT: T 1326 MET cc_start: 0.9124 (mtp) cc_final: 0.8463 (ppp) REVERT: T 1375 PHE cc_start: 0.9417 (m-10) cc_final: 0.9206 (m-80) REVERT: T 1487 MET cc_start: 0.5839 (mmp) cc_final: 0.5433 (ptp) REVERT: T 1550 LYS cc_start: 0.9122 (mtmt) cc_final: 0.8886 (mtmm) REVERT: T 1565 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: T 1618 ARG cc_start: 0.8563 (tpt170) cc_final: 0.8194 (tpt170) REVERT: T 1691 MET cc_start: 0.8065 (mtt) cc_final: 0.7830 (mtt) REVERT: T 1718 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9243 (pp) REVERT: T 1724 LYS cc_start: 0.9542 (ttmt) cc_final: 0.9323 (tppt) REVERT: T 1729 TYR cc_start: 0.8801 (t80) cc_final: 0.8566 (t80) REVERT: T 1744 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9239 (pp) REVERT: T 1750 PHE cc_start: 0.9626 (OUTLIER) cc_final: 0.8895 (p90) REVERT: T 1779 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: T 1799 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.8990 (mmp80) REVERT: T 1813 TYR cc_start: 0.9290 (t80) cc_final: 0.8990 (t80) REVERT: T 1860 PHE cc_start: 0.9352 (t80) cc_final: 0.9124 (t80) REVERT: T 1927 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6974 (p90) REVERT: T 1969 TRP cc_start: 0.8532 (m100) cc_final: 0.7819 (m100) REVERT: T 2144 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.9036 (pp20) REVERT: T 2163 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7467 (p0) REVERT: T 2171 PHE cc_start: 0.9001 (m-10) cc_final: 0.8594 (m-10) REVERT: T 2189 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8933 (m-40) REVERT: T 2215 LYS cc_start: 0.8669 (mttt) cc_final: 0.8300 (mttt) REVERT: T 2279 MET cc_start: 0.9720 (mmm) cc_final: 0.9389 (mmm) REVERT: T 2305 ARG cc_start: 0.9239 (mpt-90) cc_final: 0.8692 (mmp80) REVERT: T 2316 TYR cc_start: 0.9180 (m-80) cc_final: 0.8675 (m-80) REVERT: T 2416 MET cc_start: 0.7095 (mpp) cc_final: 0.6706 (mpp) REVERT: T 2446 ASP cc_start: 0.8980 (t0) cc_final: 0.8760 (t70) REVERT: T 2470 ASN cc_start: 0.8859 (m-40) cc_final: 0.8650 (p0) REVERT: T 2605 MET cc_start: 0.8044 (mtm) cc_final: 0.7596 (mtm) REVERT: T 2643 ILE cc_start: 0.9380 (tt) cc_final: 0.9065 (tt) REVERT: T 2695 GLU cc_start: 0.8901 (tp30) cc_final: 0.8645 (tp30) REVERT: T 2730 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8437 (tm-30) REVERT: T 2773 ARG cc_start: 0.9218 (ptm160) cc_final: 0.8753 (ttp80) REVERT: T 2784 MET cc_start: 0.8940 (tpp) cc_final: 0.8535 (tpp) REVERT: T 2897 MET cc_start: 0.8499 (ttm) cc_final: 0.8239 (ttm) REVERT: T 2959 MET cc_start: 0.9374 (pmm) cc_final: 0.9057 (pmm) REVERT: T 3022 PHE cc_start: 0.9034 (m-10) cc_final: 0.8751 (m-80) REVERT: T 3248 LEU cc_start: 0.9647 (tp) cc_final: 0.9446 (tt) REVERT: T 3558 MET cc_start: 0.8673 (mtp) cc_final: 0.8385 (mtp) REVERT: T 3562 MET cc_start: 0.9234 (ttp) cc_final: 0.8883 (ptm) outliers start: 73 outliers final: 26 residues processed: 753 average time/residue: 0.2323 time to fit residues: 290.7541 Evaluate side-chains 522 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 486 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 1506 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1614 ASN Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1644 LEU Chi-restraints excluded: chain T residue 1660 VAL Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1718 LEU Chi-restraints excluded: chain T residue 1744 LEU Chi-restraints excluded: chain T residue 1750 PHE Chi-restraints excluded: chain T residue 1779 GLN Chi-restraints excluded: chain T residue 1790 VAL Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1859 LEU Chi-restraints excluded: chain T residue 1900 LEU Chi-restraints excluded: chain T residue 1920 ILE Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1941 LEU Chi-restraints excluded: chain T residue 1949 LEU Chi-restraints excluded: chain T residue 1995 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2144 GLU Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2182 GLU Chi-restraints excluded: chain T residue 2189 ASN Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2236 ILE Chi-restraints excluded: chain T residue 2278 LEU Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2325 LEU Chi-restraints excluded: chain T residue 2556 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 87 HIS A 137 GLN A 372 HIS B 60 GLN B 95 GLN B 248 HIS B 406 HIS D 262 ASN D 360 ASN D 644 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 GLN F 580 HIS F 624 GLN ** T 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 615 ASN T 639 HIS ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 896 GLN ** T1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1105 ASN T1287 ASN T1300 ASN T1312 HIS T1407 GLN T1470 ASN T1493 GLN T1565 GLN T1571 ASN T1659 GLN ** T1768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1781 ASN T1838 HIS T1903 GLN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1981 GLN ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1992 HIS T1998 ASN ** T2009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2122 ASN T2174 ASN T2188 GLN T2189 ASN T2200 HIS T2207 GLN T2245 GLN T2266 ASN ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN T2507 ASN ** T2592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2646 ASN T2651 ASN ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2811 GLN T2861 ASN T2863 HIS T2957 HIS T3073 ASN T3154 HIS T3357 GLN ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.091000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062668 restraints weight = 172726.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064002 restraints weight = 95960.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065302 restraints weight = 61224.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065523 restraints weight = 41927.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.065584 restraints weight = 38757.899| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 41847 Z= 0.219 Angle : 0.795 12.059 56664 Z= 0.401 Chirality : 0.046 0.249 6396 Planarity : 0.005 0.068 7199 Dihedral : 6.717 57.684 5549 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.80 % Favored : 90.16 % Rotamer: Outliers : 2.78 % Allowed : 15.51 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.11), residues: 4978 helix: -0.19 (0.09), residues: 2945 sheet: -2.64 (0.33), residues: 180 loop : -3.39 (0.13), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T1054 TYR 0.029 0.002 TYR E 304 PHE 0.050 0.002 PHE T1801 TRP 0.023 0.002 TRP B 469 HIS 0.010 0.001 HIS T2010 Details of bonding type rmsd covalent geometry : bond 0.00478 (41845) covalent geometry : angle 0.79454 (56664) hydrogen bonds : bond 0.05110 ( 2230) hydrogen bonds : angle 5.11368 ( 6546) Misc. bond : bond 0.00154 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 559 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5601 (ppp) cc_final: 0.4893 (ppp) REVERT: A 111 ASN cc_start: 0.7935 (t0) cc_final: 0.6627 (t0) REVERT: A 119 MET cc_start: 0.9037 (ppp) cc_final: 0.8807 (ppp) REVERT: A 190 MET cc_start: 0.9588 (ttm) cc_final: 0.9174 (tmm) REVERT: A 361 GLU cc_start: 0.9451 (tp30) cc_final: 0.9011 (tp30) REVERT: B 98 LEU cc_start: 0.9617 (mt) cc_final: 0.9179 (mt) REVERT: B 144 THR cc_start: 0.9623 (p) cc_final: 0.9402 (t) REVERT: D 285 LEU cc_start: 0.9208 (mt) cc_final: 0.8911 (mt) REVERT: D 536 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7005 (mmmt) REVERT: D 609 GLU cc_start: 0.9079 (tp30) cc_final: 0.8539 (tm-30) REVERT: D 622 PHE cc_start: 0.8406 (m-10) cc_final: 0.8017 (m-10) REVERT: D 656 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8709 (tm-30) REVERT: D 689 GLU cc_start: 0.8597 (tp30) cc_final: 0.8376 (tp30) REVERT: E 223 LEU cc_start: 0.8671 (mt) cc_final: 0.8249 (mp) REVERT: E 266 MET cc_start: 0.9045 (mtt) cc_final: 0.8692 (mtm) REVERT: E 300 MET cc_start: 0.7806 (mmt) cc_final: 0.7016 (mmt) REVERT: F 586 LYS cc_start: 0.8339 (mppt) cc_final: 0.7890 (mmtm) REVERT: F 621 ASP cc_start: 0.8853 (t0) cc_final: 0.8541 (t0) REVERT: F 625 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7090 (pm20) REVERT: T 119 MET cc_start: 0.2632 (mmt) cc_final: 0.2144 (mmt) REVERT: T 352 ARG cc_start: 0.9235 (ptt-90) cc_final: 0.8890 (ptm-80) REVERT: T 593 PHE cc_start: 0.9269 (m-80) cc_final: 0.9049 (m-80) REVERT: T 689 MET cc_start: 0.8942 (mtt) cc_final: 0.8673 (mpp) REVERT: T 691 MET cc_start: 0.9196 (mmm) cc_final: 0.8686 (mmm) REVERT: T 711 GLU cc_start: 0.9755 (tp30) cc_final: 0.9429 (tp30) REVERT: T 749 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8651 (tppt) REVERT: T 771 MET cc_start: 0.8573 (mmt) cc_final: 0.8305 (mmt) REVERT: T 775 LEU cc_start: 0.8954 (pp) cc_final: 0.8656 (pp) REVERT: T 840 GLN cc_start: 0.8455 (pt0) cc_final: 0.7890 (tm-30) REVERT: T 844 GLN cc_start: 0.8931 (pm20) cc_final: 0.8619 (pm20) REVERT: T 853 HIS cc_start: 0.7904 (m90) cc_final: 0.7343 (m90) REVERT: T 856 GLU cc_start: 0.8751 (pp20) cc_final: 0.8500 (pp20) REVERT: T 965 ASP cc_start: 0.9016 (p0) cc_final: 0.8766 (p0) REVERT: T 1071 ASP cc_start: 0.9579 (OUTLIER) cc_final: 0.9317 (t0) REVERT: T 1084 GLU cc_start: 0.8672 (pp20) cc_final: 0.8410 (pp20) REVERT: T 1113 LEU cc_start: 0.9453 (mt) cc_final: 0.9244 (mt) REVERT: T 1130 ASN cc_start: 0.8755 (t0) cc_final: 0.8550 (t0) REVERT: T 1133 LEU cc_start: 0.9038 (tp) cc_final: 0.8661 (tp) REVERT: T 1147 ASP cc_start: 0.9019 (t0) cc_final: 0.8437 (t70) REVERT: T 1246 LYS cc_start: 0.9650 (mtmt) cc_final: 0.9349 (mtpp) REVERT: T 1266 ASP cc_start: 0.9483 (m-30) cc_final: 0.9252 (m-30) REVERT: T 1326 MET cc_start: 0.9102 (mtp) cc_final: 0.8471 (ppp) REVERT: T 1487 MET cc_start: 0.5973 (mmp) cc_final: 0.5703 (ptp) REVERT: T 1517 GLU cc_start: 0.1753 (OUTLIER) cc_final: 0.1504 (pp20) REVERT: T 1568 MET cc_start: 0.8443 (tmm) cc_final: 0.8112 (tmm) REVERT: T 1729 TYR cc_start: 0.8701 (t80) cc_final: 0.8460 (t80) REVERT: T 1813 TYR cc_start: 0.9326 (t80) cc_final: 0.8965 (t80) REVERT: T 1969 TRP cc_start: 0.8520 (m100) cc_final: 0.7968 (m100) REVERT: T 2171 PHE cc_start: 0.9036 (m-10) cc_final: 0.8694 (m-80) REVERT: T 2215 LYS cc_start: 0.8754 (mttt) cc_final: 0.8545 (mttt) REVERT: T 2279 MET cc_start: 0.9602 (mmm) cc_final: 0.9192 (mmm) REVERT: T 2305 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8799 (mmm160) REVERT: T 2312 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8428 (mt-10) REVERT: T 2342 HIS cc_start: 0.9042 (m-70) cc_final: 0.8799 (m-70) REVERT: T 2359 TRP cc_start: 0.7744 (m100) cc_final: 0.7466 (m100) REVERT: T 2416 MET cc_start: 0.7227 (mpp) cc_final: 0.6758 (mpp) REVERT: T 2446 ASP cc_start: 0.8994 (t0) cc_final: 0.8731 (t0) REVERT: T 2604 ASN cc_start: 0.8463 (m110) cc_final: 0.8151 (t0) REVERT: T 2605 MET cc_start: 0.8035 (mtm) cc_final: 0.7616 (mtm) REVERT: T 2635 GLN cc_start: 0.9192 (mp10) cc_final: 0.8770 (mp10) REVERT: T 2695 GLU cc_start: 0.8987 (tp30) cc_final: 0.8662 (tp30) REVERT: T 2773 ARG cc_start: 0.9135 (ptm160) cc_final: 0.8584 (ttp80) REVERT: T 2784 MET cc_start: 0.8858 (tpp) cc_final: 0.8484 (tpp) REVERT: T 2897 MET cc_start: 0.8456 (ttm) cc_final: 0.8189 (ttm) REVERT: T 2959 MET cc_start: 0.9341 (pmm) cc_final: 0.9012 (pmm) REVERT: T 3022 PHE cc_start: 0.9059 (m-10) cc_final: 0.8571 (m-80) REVERT: T 3283 PHE cc_start: 0.8856 (m-80) cc_final: 0.8606 (t80) REVERT: T 3322 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8314 (tm-30) REVERT: T 3391 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8763 (pt) REVERT: T 3418 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8338 (mtm-85) REVERT: T 3558 MET cc_start: 0.8793 (mtp) cc_final: 0.8510 (mtp) REVERT: T 3562 MET cc_start: 0.9213 (ttp) cc_final: 0.8813 (ptm) outliers start: 127 outliers final: 66 residues processed: 647 average time/residue: 0.2182 time to fit residues: 238.0451 Evaluate side-chains 549 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 477 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 582 PHE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 693 MET Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1171 ILE Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1517 GLU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1588 LEU Chi-restraints excluded: chain T residue 1644 LEU Chi-restraints excluded: chain T residue 1663 VAL Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1900 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2026 THR Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3391 LEU Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3653 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 55 optimal weight: 8.9990 chunk 449 optimal weight: 5.9990 chunk 186 optimal weight: 30.0000 chunk 399 optimal weight: 3.9990 chunk 174 optimal weight: 50.0000 chunk 407 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 465 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 115 ASN B 406 HIS D 360 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1074 ASN ** T1768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2188 GLN ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2948 ASN ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.090918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.062752 restraints weight = 171840.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064159 restraints weight = 98808.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065185 restraints weight = 58179.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065236 restraints weight = 44505.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.065779 restraints weight = 42824.757| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41847 Z= 0.201 Angle : 0.768 14.181 56664 Z= 0.386 Chirality : 0.045 0.291 6396 Planarity : 0.005 0.064 7199 Dihedral : 6.291 57.363 5495 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.90 % Favored : 90.06 % Rotamer: Outliers : 3.33 % Allowed : 18.38 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.12), residues: 4978 helix: 0.09 (0.09), residues: 2951 sheet: -2.21 (0.35), residues: 175 loop : -3.16 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T2599 TYR 0.036 0.002 TYR T3358 PHE 0.059 0.002 PHE T1927 TRP 0.022 0.002 TRP T2460 HIS 0.012 0.001 HIS T1992 Details of bonding type rmsd covalent geometry : bond 0.00439 (41845) covalent geometry : angle 0.76788 (56664) hydrogen bonds : bond 0.04649 ( 2230) hydrogen bonds : angle 4.97780 ( 6546) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 517 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.9110 (ppp) cc_final: 0.8883 (ppp) REVERT: A 190 MET cc_start: 0.9599 (ttm) cc_final: 0.9174 (tmm) REVERT: A 227 MET cc_start: 0.9074 (mmm) cc_final: 0.8766 (mmm) REVERT: A 361 GLU cc_start: 0.9461 (tp30) cc_final: 0.9022 (tp30) REVERT: B 98 LEU cc_start: 0.9583 (mt) cc_final: 0.9136 (mt) REVERT: B 144 THR cc_start: 0.9614 (p) cc_final: 0.9395 (t) REVERT: B 282 ASN cc_start: 0.9450 (OUTLIER) cc_final: 0.9055 (m-40) REVERT: B 425 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8930 (tpp) REVERT: B 468 LEU cc_start: 0.9110 (tt) cc_final: 0.8751 (pp) REVERT: D 36 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7898 (pmt-80) REVERT: D 285 LEU cc_start: 0.9237 (mt) cc_final: 0.8950 (mt) REVERT: D 536 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7041 (mmmt) REVERT: D 537 LYS cc_start: 0.8408 (tttt) cc_final: 0.8077 (tttp) REVERT: D 609 GLU cc_start: 0.9114 (tp30) cc_final: 0.8556 (tm-30) REVERT: D 656 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8644 (tm-30) REVERT: D 657 GLU cc_start: 0.9424 (tt0) cc_final: 0.9147 (tt0) REVERT: D 689 GLU cc_start: 0.8678 (tp30) cc_final: 0.8448 (tp30) REVERT: E 266 MET cc_start: 0.9033 (mtt) cc_final: 0.8690 (mtm) REVERT: E 274 GLU cc_start: 0.9246 (tp30) cc_final: 0.9037 (tp30) REVERT: E 300 MET cc_start: 0.7882 (mmt) cc_final: 0.7285 (mmt) REVERT: F 586 LYS cc_start: 0.8232 (mppt) cc_final: 0.7831 (mmtm) REVERT: F 621 ASP cc_start: 0.8906 (t0) cc_final: 0.8596 (t0) REVERT: F 625 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: T 35 MET cc_start: 0.5445 (ttp) cc_final: 0.5112 (ptt) REVERT: T 352 ARG cc_start: 0.9223 (ptt-90) cc_final: 0.8986 (ptp-170) REVERT: T 598 ILE cc_start: 0.9238 (pt) cc_final: 0.8330 (mm) REVERT: T 691 MET cc_start: 0.9181 (mmm) cc_final: 0.8690 (mmm) REVERT: T 711 GLU cc_start: 0.9746 (tp30) cc_final: 0.9423 (tp30) REVERT: T 749 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8607 (tppt) REVERT: T 771 MET cc_start: 0.8585 (mmt) cc_final: 0.8282 (mmt) REVERT: T 775 LEU cc_start: 0.8985 (pp) cc_final: 0.8642 (pp) REVERT: T 781 GLU cc_start: 0.8993 (pm20) cc_final: 0.8774 (pm20) REVERT: T 840 GLN cc_start: 0.8469 (pt0) cc_final: 0.7931 (tm-30) REVERT: T 844 GLN cc_start: 0.8967 (pm20) cc_final: 0.8643 (pm20) REVERT: T 965 ASP cc_start: 0.9040 (p0) cc_final: 0.8804 (p0) REVERT: T 1084 GLU cc_start: 0.8659 (pp20) cc_final: 0.8392 (pp20) REVERT: T 1113 LEU cc_start: 0.9435 (mt) cc_final: 0.9226 (mt) REVERT: T 1130 ASN cc_start: 0.8694 (t0) cc_final: 0.8466 (t0) REVERT: T 1133 LEU cc_start: 0.9029 (tp) cc_final: 0.8548 (tp) REVERT: T 1147 ASP cc_start: 0.9026 (t0) cc_final: 0.8536 (t70) REVERT: T 1246 LYS cc_start: 0.9646 (mtmt) cc_final: 0.9400 (mtpp) REVERT: T 1266 ASP cc_start: 0.9472 (m-30) cc_final: 0.9233 (m-30) REVERT: T 1326 MET cc_start: 0.9109 (mtp) cc_final: 0.8474 (ppp) REVERT: T 1506 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5507 (pp) REVERT: T 1547 MET cc_start: 0.8677 (mmp) cc_final: 0.8435 (mmp) REVERT: T 1568 MET cc_start: 0.8511 (tmm) cc_final: 0.8305 (tmm) REVERT: T 1586 LEU cc_start: 0.9388 (mp) cc_final: 0.8802 (tt) REVERT: T 1666 PHE cc_start: 0.9559 (OUTLIER) cc_final: 0.9303 (m-10) REVERT: T 1813 TYR cc_start: 0.9312 (t80) cc_final: 0.8958 (t80) REVERT: T 2163 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7684 (p0) REVERT: T 2171 PHE cc_start: 0.9047 (m-10) cc_final: 0.8708 (m-10) REVERT: T 2215 LYS cc_start: 0.8765 (mttt) cc_final: 0.8458 (mttt) REVERT: T 2279 MET cc_start: 0.9582 (mmm) cc_final: 0.9226 (mmm) REVERT: T 2305 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (mmm160) REVERT: T 2316 TYR cc_start: 0.8676 (m-80) cc_final: 0.8356 (m-80) REVERT: T 2342 HIS cc_start: 0.9044 (m-70) cc_final: 0.8788 (m-70) REVERT: T 2359 TRP cc_start: 0.7850 (m100) cc_final: 0.7557 (m100) REVERT: T 2416 MET cc_start: 0.7386 (mpp) cc_final: 0.6835 (mpp) REVERT: T 2446 ASP cc_start: 0.9027 (t0) cc_final: 0.8724 (t70) REVERT: T 2530 MET cc_start: 0.9398 (mmp) cc_final: 0.9092 (mmm) REVERT: T 2604 ASN cc_start: 0.8498 (m110) cc_final: 0.8097 (t0) REVERT: T 2605 MET cc_start: 0.8027 (mtm) cc_final: 0.7557 (mtm) REVERT: T 2624 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8654 (mmmm) REVERT: T 2695 GLU cc_start: 0.8943 (tp30) cc_final: 0.8680 (tp30) REVERT: T 2773 ARG cc_start: 0.9183 (ptm160) cc_final: 0.8598 (ttp80) REVERT: T 2784 MET cc_start: 0.8897 (tpp) cc_final: 0.8515 (tpp) REVERT: T 2897 MET cc_start: 0.8437 (ttm) cc_final: 0.8188 (ttm) REVERT: T 2959 MET cc_start: 0.9301 (pmm) cc_final: 0.8905 (pmm) REVERT: T 3022 PHE cc_start: 0.8955 (m-10) cc_final: 0.8596 (m-80) REVERT: T 3093 LYS cc_start: 0.8968 (ptpt) cc_final: 0.8727 (ptpt) REVERT: T 3248 LEU cc_start: 0.9634 (tp) cc_final: 0.9213 (tt) REVERT: T 3558 MET cc_start: 0.8831 (mtp) cc_final: 0.8528 (mtp) REVERT: T 3562 MET cc_start: 0.9210 (ttp) cc_final: 0.8795 (ptm) REVERT: T 3576 LYS cc_start: 0.9305 (mtmt) cc_final: 0.9033 (mtmm) REVERT: T 3737 ASP cc_start: 0.8835 (t0) cc_final: 0.8625 (t0) outliers start: 152 outliers final: 88 residues processed: 630 average time/residue: 0.2197 time to fit residues: 234.7893 Evaluate side-chains 571 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 474 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 740 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1171 ILE Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1506 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1666 PHE Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1904 SER Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2188 GLN Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2384 ILE Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2856 THR Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 40 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 497 optimal weight: 0.6980 chunk 212 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 473 optimal weight: 4.9990 chunk 441 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 22 GLN ** T 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 401 ASN ** T1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1074 ASN ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1654 ASN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2189 ASN ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.090070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061086 restraints weight = 173041.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.063035 restraints weight = 95124.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063976 restraints weight = 56589.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064622 restraints weight = 39831.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.064702 restraints weight = 35415.238| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41847 Z= 0.220 Angle : 0.772 13.739 56664 Z= 0.388 Chirality : 0.045 0.266 6396 Planarity : 0.005 0.067 7199 Dihedral : 6.220 57.082 5489 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.04 % Favored : 89.94 % Rotamer: Outliers : 4.05 % Allowed : 19.97 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.12), residues: 4978 helix: 0.23 (0.09), residues: 2943 sheet: -1.99 (0.35), residues: 181 loop : -3.04 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T2599 TYR 0.042 0.002 TYR T3358 PHE 0.065 0.002 PHE T1767 TRP 0.032 0.002 TRP T2179 HIS 0.016 0.001 HIS T2010 Details of bonding type rmsd covalent geometry : bond 0.00480 (41845) covalent geometry : angle 0.77246 (56664) hydrogen bonds : bond 0.04521 ( 2230) hydrogen bonds : angle 4.98373 ( 6546) Misc. bond : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 508 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9593 (ttm) cc_final: 0.9178 (tmm) REVERT: A 227 MET cc_start: 0.9177 (mmm) cc_final: 0.8899 (mmm) REVERT: A 355 MET cc_start: 0.8907 (mmt) cc_final: 0.8027 (mmt) REVERT: A 361 GLU cc_start: 0.9464 (tp30) cc_final: 0.9014 (tp30) REVERT: B 144 THR cc_start: 0.9644 (p) cc_final: 0.9417 (t) REVERT: B 282 ASN cc_start: 0.9462 (OUTLIER) cc_final: 0.9012 (m-40) REVERT: B 425 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8982 (tpp) REVERT: B 468 LEU cc_start: 0.9112 (tt) cc_final: 0.8765 (pp) REVERT: D 285 LEU cc_start: 0.9235 (mt) cc_final: 0.8950 (mt) REVERT: D 536 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7047 (mmmt) REVERT: D 537 LYS cc_start: 0.8398 (tttt) cc_final: 0.8083 (tttp) REVERT: D 573 ARG cc_start: 0.8584 (ptt90) cc_final: 0.8285 (ptm-80) REVERT: D 609 GLU cc_start: 0.9121 (tp30) cc_final: 0.8567 (tm-30) REVERT: D 622 PHE cc_start: 0.8451 (m-10) cc_final: 0.8117 (m-10) REVERT: D 656 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8649 (tm-30) REVERT: D 689 GLU cc_start: 0.8708 (tp30) cc_final: 0.8474 (tp30) REVERT: E 274 GLU cc_start: 0.9244 (tp30) cc_final: 0.8987 (tp30) REVERT: E 300 MET cc_start: 0.7841 (mmt) cc_final: 0.7310 (mmt) REVERT: F 621 ASP cc_start: 0.8965 (t0) cc_final: 0.8574 (t0) REVERT: F 625 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: T 35 MET cc_start: 0.5154 (ttp) cc_final: 0.4921 (ptt) REVERT: T 352 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8959 (ptp-170) REVERT: T 390 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8859 (pp) REVERT: T 483 ASP cc_start: 0.9525 (t0) cc_final: 0.9305 (p0) REVERT: T 591 MET cc_start: 0.9466 (mmt) cc_final: 0.9136 (ttm) REVERT: T 691 MET cc_start: 0.9174 (mmm) cc_final: 0.8600 (mmm) REVERT: T 711 GLU cc_start: 0.9745 (tp30) cc_final: 0.9404 (tp30) REVERT: T 749 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8623 (tppt) REVERT: T 768 LEU cc_start: 0.9470 (mm) cc_final: 0.9269 (mm) REVERT: T 771 MET cc_start: 0.8608 (mmt) cc_final: 0.8312 (mmt) REVERT: T 775 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8689 (pp) REVERT: T 781 GLU cc_start: 0.8995 (pm20) cc_final: 0.8758 (pm20) REVERT: T 840 GLN cc_start: 0.8461 (pt0) cc_final: 0.8247 (tm-30) REVERT: T 853 HIS cc_start: 0.7855 (m90) cc_final: 0.7339 (m90) REVERT: T 856 GLU cc_start: 0.8771 (pp20) cc_final: 0.8387 (pp20) REVERT: T 889 GLN cc_start: 0.8234 (mp10) cc_final: 0.8027 (mp10) REVERT: T 965 ASP cc_start: 0.8987 (p0) cc_final: 0.8712 (p0) REVERT: T 1084 GLU cc_start: 0.8675 (pp20) cc_final: 0.8386 (pp20) REVERT: T 1113 LEU cc_start: 0.9392 (mt) cc_final: 0.9166 (mt) REVERT: T 1130 ASN cc_start: 0.8643 (t0) cc_final: 0.8390 (t0) REVERT: T 1133 LEU cc_start: 0.9029 (tp) cc_final: 0.8546 (tp) REVERT: T 1147 ASP cc_start: 0.9047 (t0) cc_final: 0.8570 (t70) REVERT: T 1246 LYS cc_start: 0.9651 (mtmt) cc_final: 0.9356 (mtpp) REVERT: T 1248 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8152 (p) REVERT: T 1266 ASP cc_start: 0.9459 (m-30) cc_final: 0.9225 (m-30) REVERT: T 1326 MET cc_start: 0.9114 (mtp) cc_final: 0.8461 (ppp) REVERT: T 1506 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5432 (pp) REVERT: T 1586 LEU cc_start: 0.9341 (mp) cc_final: 0.8889 (tt) REVERT: T 1615 MET cc_start: 0.6666 (mtp) cc_final: 0.6264 (mtp) REVERT: T 1813 TYR cc_start: 0.9331 (t80) cc_final: 0.8986 (t80) REVERT: T 1957 MET cc_start: 0.8061 (ttm) cc_final: 0.7775 (tmm) REVERT: T 2163 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7791 (p0) REVERT: T 2171 PHE cc_start: 0.9043 (m-10) cc_final: 0.8736 (m-80) REVERT: T 2215 LYS cc_start: 0.8671 (mttt) cc_final: 0.8324 (mtmt) REVERT: T 2279 MET cc_start: 0.9609 (mmm) cc_final: 0.9248 (mmm) REVERT: T 2305 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8743 (mmm160) REVERT: T 2316 TYR cc_start: 0.8718 (m-80) cc_final: 0.8397 (m-80) REVERT: T 2342 HIS cc_start: 0.9083 (m-70) cc_final: 0.8843 (m-70) REVERT: T 2359 TRP cc_start: 0.7911 (m100) cc_final: 0.7672 (m100) REVERT: T 2416 MET cc_start: 0.7482 (mpp) cc_final: 0.6892 (mpp) REVERT: T 2446 ASP cc_start: 0.9021 (t0) cc_final: 0.8714 (t70) REVERT: T 2530 MET cc_start: 0.9391 (mmp) cc_final: 0.9087 (mmm) REVERT: T 2604 ASN cc_start: 0.8518 (m110) cc_final: 0.8010 (t0) REVERT: T 2605 MET cc_start: 0.8054 (mtm) cc_final: 0.7531 (mtm) REVERT: T 2624 LYS cc_start: 0.8950 (mmmm) cc_final: 0.8642 (mmmm) REVERT: T 2670 GLN cc_start: 0.8915 (mt0) cc_final: 0.8500 (mm-40) REVERT: T 2695 GLU cc_start: 0.8889 (tp30) cc_final: 0.8654 (tp30) REVERT: T 2773 ARG cc_start: 0.9145 (ptm160) cc_final: 0.8600 (ttp80) REVERT: T 2784 MET cc_start: 0.8852 (tpp) cc_final: 0.8442 (tpp) REVERT: T 2897 MET cc_start: 0.8386 (ttm) cc_final: 0.8124 (ttm) REVERT: T 2959 MET cc_start: 0.9288 (pmm) cc_final: 0.9042 (pmm) REVERT: T 3022 PHE cc_start: 0.9010 (m-10) cc_final: 0.8548 (m-80) REVERT: T 3093 LYS cc_start: 0.9007 (ptpt) cc_final: 0.8781 (ptpt) REVERT: T 3283 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8728 (t80) REVERT: T 3558 MET cc_start: 0.8823 (mtp) cc_final: 0.8504 (mtp) REVERT: T 3576 LYS cc_start: 0.9336 (mtmt) cc_final: 0.9028 (mtmm) REVERT: T 3737 ASP cc_start: 0.8811 (t0) cc_final: 0.8595 (t0) outliers start: 185 outliers final: 116 residues processed: 640 average time/residue: 0.2128 time to fit residues: 232.0487 Evaluate side-chains 598 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 470 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 352 ARG Chi-restraints excluded: chain T residue 354 ILE Chi-restraints excluded: chain T residue 390 LEU Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 740 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1074 ASN Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1171 ILE Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1506 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1695 LEU Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2026 THR Chi-restraints excluded: chain T residue 2027 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2377 THR Chi-restraints excluded: chain T residue 2384 ILE Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2611 SER Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2856 THR Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3156 LEU Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3241 THR Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 83 optimal weight: 20.0000 chunk 310 optimal weight: 1.9990 chunk 393 optimal weight: 0.6980 chunk 440 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 249 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 37 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 354 GLN B 406 HIS ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 150 ASN ** T1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1074 ASN ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1987 GLN T2009 HIS ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2189 ASN ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2896 ASN T2907 HIS ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3471 HIS ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.091604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062284 restraints weight = 170800.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.064061 restraints weight = 90513.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065336 restraints weight = 58907.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.066055 restraints weight = 44154.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066651 restraints weight = 37069.836| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41847 Z= 0.155 Angle : 0.743 13.719 56664 Z= 0.369 Chirality : 0.044 0.208 6396 Planarity : 0.005 0.076 7199 Dihedral : 5.995 55.711 5489 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.32 % Favored : 90.64 % Rotamer: Outliers : 3.43 % Allowed : 21.37 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.45 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.12), residues: 4978 helix: 0.43 (0.10), residues: 2947 sheet: -1.77 (0.35), residues: 187 loop : -2.93 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 36 TYR 0.022 0.001 TYR D 258 PHE 0.054 0.002 PHE T1767 TRP 0.036 0.002 TRP T2179 HIS 0.011 0.001 HIS T1768 Details of bonding type rmsd covalent geometry : bond 0.00341 (41845) covalent geometry : angle 0.74297 (56664) hydrogen bonds : bond 0.04254 ( 2230) hydrogen bonds : angle 4.79890 ( 6546) Misc. bond : bond 0.00168 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 545 time to evaluate : 1.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9586 (ttm) cc_final: 0.9129 (tmm) REVERT: A 355 MET cc_start: 0.8753 (mmt) cc_final: 0.8075 (mmt) REVERT: A 361 GLU cc_start: 0.9469 (tp30) cc_final: 0.9061 (tp30) REVERT: B 98 LEU cc_start: 0.9563 (mt) cc_final: 0.9112 (mt) REVERT: B 144 THR cc_start: 0.9607 (p) cc_final: 0.9370 (t) REVERT: B 282 ASN cc_start: 0.9447 (OUTLIER) cc_final: 0.8832 (m-40) REVERT: D 285 LEU cc_start: 0.9243 (mt) cc_final: 0.8959 (mt) REVERT: D 536 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7031 (mmmt) REVERT: D 537 LYS cc_start: 0.8337 (tttt) cc_final: 0.8036 (tttp) REVERT: D 573 ARG cc_start: 0.8550 (ptt90) cc_final: 0.8337 (ptm-80) REVERT: D 609 GLU cc_start: 0.9118 (tp30) cc_final: 0.8573 (tm-30) REVERT: D 656 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8598 (tm-30) REVERT: D 657 GLU cc_start: 0.9407 (tt0) cc_final: 0.9066 (tt0) REVERT: D 689 GLU cc_start: 0.8753 (tp30) cc_final: 0.8514 (tp30) REVERT: E 269 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8085 (pptt) REVERT: E 274 GLU cc_start: 0.9140 (tp30) cc_final: 0.8855 (tp30) REVERT: E 300 MET cc_start: 0.7779 (mmt) cc_final: 0.7252 (mmt) REVERT: E 302 GLN cc_start: 0.9366 (tp40) cc_final: 0.9045 (tp40) REVERT: F 549 MET cc_start: 0.8831 (mmm) cc_final: 0.8547 (mtp) REVERT: F 586 LYS cc_start: 0.8028 (mppt) cc_final: 0.7744 (mmtm) REVERT: F 621 ASP cc_start: 0.8941 (t0) cc_final: 0.8550 (t0) REVERT: F 625 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7256 (pm20) REVERT: T 83 PHE cc_start: 0.8609 (t80) cc_final: 0.8291 (t80) REVERT: T 352 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8956 (ptp-170) REVERT: T 390 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8756 (pp) REVERT: T 474 ARG cc_start: 0.9632 (tpt90) cc_final: 0.8906 (mmm160) REVERT: T 691 MET cc_start: 0.9200 (mmm) cc_final: 0.8689 (mmm) REVERT: T 711 GLU cc_start: 0.9761 (tp30) cc_final: 0.9430 (tp30) REVERT: T 749 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8596 (tppt) REVERT: T 771 MET cc_start: 0.8589 (mmt) cc_final: 0.8265 (mmt) REVERT: T 775 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8664 (pp) REVERT: T 781 GLU cc_start: 0.8941 (pm20) cc_final: 0.8733 (pm20) REVERT: T 965 ASP cc_start: 0.8988 (p0) cc_final: 0.8691 (p0) REVERT: T 1084 GLU cc_start: 0.8682 (pp20) cc_final: 0.8353 (pp20) REVERT: T 1130 ASN cc_start: 0.8545 (t0) cc_final: 0.8274 (t0) REVERT: T 1133 LEU cc_start: 0.8994 (tp) cc_final: 0.8479 (tp) REVERT: T 1147 ASP cc_start: 0.9048 (t0) cc_final: 0.8544 (t70) REVERT: T 1246 LYS cc_start: 0.9646 (mtmt) cc_final: 0.9352 (mtpp) REVERT: T 1266 ASP cc_start: 0.9457 (m-30) cc_final: 0.9213 (m-30) REVERT: T 1326 MET cc_start: 0.9110 (mtp) cc_final: 0.8385 (ppp) REVERT: T 1586 LEU cc_start: 0.9327 (mp) cc_final: 0.8886 (tt) REVERT: T 1615 MET cc_start: 0.6656 (mtp) cc_final: 0.6311 (mtp) REVERT: T 1813 TYR cc_start: 0.9322 (t80) cc_final: 0.8987 (t80) REVERT: T 1903 GLN cc_start: 0.9612 (tt0) cc_final: 0.9374 (tt0) REVERT: T 1907 LEU cc_start: 0.8522 (pp) cc_final: 0.8316 (pp) REVERT: T 1937 GLU cc_start: 0.8647 (mp0) cc_final: 0.8431 (mp0) REVERT: T 2163 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7835 (p0) REVERT: T 2171 PHE cc_start: 0.9034 (m-10) cc_final: 0.8722 (m-80) REVERT: T 2215 LYS cc_start: 0.8663 (mttt) cc_final: 0.8330 (mtmt) REVERT: T 2279 MET cc_start: 0.9610 (mmm) cc_final: 0.9233 (mmm) REVERT: T 2305 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.8659 (mmm160) REVERT: T 2316 TYR cc_start: 0.8734 (m-80) cc_final: 0.8499 (m-80) REVERT: T 2342 HIS cc_start: 0.9127 (m-70) cc_final: 0.8915 (m-70) REVERT: T 2387 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: T 2416 MET cc_start: 0.7426 (mpp) cc_final: 0.6884 (mpp) REVERT: T 2446 ASP cc_start: 0.9030 (t0) cc_final: 0.8706 (t70) REVERT: T 2507 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7996 (m110) REVERT: T 2530 MET cc_start: 0.9422 (mmp) cc_final: 0.9123 (mmm) REVERT: T 2605 MET cc_start: 0.7992 (mtm) cc_final: 0.7590 (mtm) REVERT: T 2624 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8542 (mmmm) REVERT: T 2695 GLU cc_start: 0.8912 (tp30) cc_final: 0.8639 (tp30) REVERT: T 2731 ASP cc_start: 0.8789 (m-30) cc_final: 0.8472 (t0) REVERT: T 2773 ARG cc_start: 0.9128 (ptm160) cc_final: 0.8611 (ttp80) REVERT: T 2784 MET cc_start: 0.8842 (tpp) cc_final: 0.8610 (mmm) REVERT: T 2792 GLN cc_start: 0.9319 (tt0) cc_final: 0.8907 (tt0) REVERT: T 2852 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: T 2897 MET cc_start: 0.8374 (ttm) cc_final: 0.8128 (ttm) REVERT: T 2959 MET cc_start: 0.9144 (pmm) cc_final: 0.8873 (pmm) REVERT: T 3022 PHE cc_start: 0.8928 (m-10) cc_final: 0.8488 (m-80) REVERT: T 3091 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9229 (tt) REVERT: T 3093 LYS cc_start: 0.9015 (ptpt) cc_final: 0.8773 (ptpt) REVERT: T 3283 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8739 (t80) REVERT: T 3499 ASP cc_start: 0.7498 (p0) cc_final: 0.7293 (p0) REVERT: T 3558 MET cc_start: 0.8841 (mtp) cc_final: 0.8543 (mtp) REVERT: T 3562 MET cc_start: 0.9123 (ttp) cc_final: 0.8843 (ptm) REVERT: T 3576 LYS cc_start: 0.9289 (mtmt) cc_final: 0.8975 (mtmm) REVERT: T 3737 ASP cc_start: 0.8800 (t0) cc_final: 0.8562 (t0) outliers start: 157 outliers final: 99 residues processed: 664 average time/residue: 0.2167 time to fit residues: 245.8834 Evaluate side-chains 603 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 490 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 352 ARG Chi-restraints excluded: chain T residue 390 LEU Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 739 ILE Chi-restraints excluded: chain T residue 740 LEU Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1074 ASN Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1171 ILE Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1695 LEU Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2027 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2387 GLU Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2507 ASN Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3653 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 476 optimal weight: 3.9990 chunk 428 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 219 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 446 optimal weight: 8.9990 chunk 308 optimal weight: 30.0000 chunk 191 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 498 optimal weight: 8.9990 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 354 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 956 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1074 ASN ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1626 ASN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2839 HIS T3073 ASN ** T3250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.089280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.060833 restraints weight = 173417.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062626 restraints weight = 99991.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063810 restraints weight = 56248.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063919 restraints weight = 48771.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063917 restraints weight = 42380.157| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 41847 Z= 0.262 Angle : 0.804 13.636 56664 Z= 0.403 Chirality : 0.046 0.262 6396 Planarity : 0.005 0.088 7199 Dihedral : 6.143 56.236 5489 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.45 % Favored : 89.53 % Rotamer: Outliers : 4.48 % Allowed : 21.90 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.12), residues: 4978 helix: 0.38 (0.09), residues: 2954 sheet: -1.70 (0.37), residues: 175 loop : -2.96 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T2599 TYR 0.025 0.002 TYR F 584 PHE 0.051 0.002 PHE T1767 TRP 0.037 0.002 TRP T2179 HIS 0.010 0.001 HIS T1768 Details of bonding type rmsd covalent geometry : bond 0.00565 (41845) covalent geometry : angle 0.80395 (56664) hydrogen bonds : bond 0.04445 ( 2230) hydrogen bonds : angle 5.00593 ( 6546) Misc. bond : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 483 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9589 (ttm) cc_final: 0.9189 (tmm) REVERT: A 227 MET cc_start: 0.8941 (mmm) cc_final: 0.8618 (mmm) REVERT: A 355 MET cc_start: 0.8758 (mmt) cc_final: 0.8428 (mmt) REVERT: A 361 GLU cc_start: 0.9432 (tp30) cc_final: 0.8983 (tp30) REVERT: B 144 THR cc_start: 0.9637 (p) cc_final: 0.9378 (t) REVERT: B 425 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.9012 (tpp) REVERT: B 444 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8362 (m170) REVERT: D 285 LEU cc_start: 0.9261 (mt) cc_final: 0.9043 (mt) REVERT: D 536 LYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7203 (mmmt) REVERT: D 537 LYS cc_start: 0.8371 (tttt) cc_final: 0.8030 (tttp) REVERT: D 573 ARG cc_start: 0.8598 (ptt90) cc_final: 0.8328 (ptm-80) REVERT: D 609 GLU cc_start: 0.9159 (tp30) cc_final: 0.8612 (tm-30) REVERT: D 622 PHE cc_start: 0.8479 (m-10) cc_final: 0.8161 (m-10) REVERT: D 656 GLN cc_start: 0.9173 (tp-100) cc_final: 0.8593 (tm-30) REVERT: D 689 GLU cc_start: 0.8715 (tp30) cc_final: 0.8483 (tp30) REVERT: E 300 MET cc_start: 0.7944 (mmt) cc_final: 0.7394 (mmt) REVERT: E 302 GLN cc_start: 0.9398 (tp40) cc_final: 0.9021 (tp40) REVERT: F 549 MET cc_start: 0.8725 (mmm) cc_final: 0.8471 (mtp) REVERT: F 621 ASP cc_start: 0.8994 (t0) cc_final: 0.8551 (t0) REVERT: F 625 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: T 83 PHE cc_start: 0.8600 (t80) cc_final: 0.8336 (t80) REVERT: T 474 ARG cc_start: 0.9623 (tpt90) cc_final: 0.8876 (mmm160) REVERT: T 570 LEU cc_start: 0.8814 (pt) cc_final: 0.8588 (pt) REVERT: T 591 MET cc_start: 0.9446 (mmt) cc_final: 0.9114 (ttp) REVERT: T 691 MET cc_start: 0.9225 (mmm) cc_final: 0.8703 (mmm) REVERT: T 711 GLU cc_start: 0.9749 (tp30) cc_final: 0.9445 (tp30) REVERT: T 749 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8635 (tppt) REVERT: T 771 MET cc_start: 0.8631 (mmt) cc_final: 0.8315 (mmt) REVERT: T 775 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8722 (pp) REVERT: T 965 ASP cc_start: 0.9012 (p0) cc_final: 0.8707 (p0) REVERT: T 1084 GLU cc_start: 0.8699 (pp20) cc_final: 0.8431 (pp20) REVERT: T 1130 ASN cc_start: 0.8593 (t0) cc_final: 0.8343 (t0) REVERT: T 1133 LEU cc_start: 0.9079 (tp) cc_final: 0.8591 (tp) REVERT: T 1147 ASP cc_start: 0.9060 (t0) cc_final: 0.8556 (t70) REVERT: T 1246 LYS cc_start: 0.9640 (mtmt) cc_final: 0.9334 (mtpp) REVERT: T 1248 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8132 (p) REVERT: T 1266 ASP cc_start: 0.9427 (m-30) cc_final: 0.9193 (m-30) REVERT: T 1326 MET cc_start: 0.9112 (mtp) cc_final: 0.8505 (ppp) REVERT: T 1586 LEU cc_start: 0.9306 (mp) cc_final: 0.8859 (tt) REVERT: T 1615 MET cc_start: 0.6844 (mtp) cc_final: 0.6505 (mtp) REVERT: T 1813 TYR cc_start: 0.9347 (t80) cc_final: 0.9004 (t80) REVERT: T 1842 TRP cc_start: 0.8123 (m100) cc_final: 0.7882 (m100) REVERT: T 1903 GLN cc_start: 0.9612 (tt0) cc_final: 0.9374 (tt0) REVERT: T 1907 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8283 (pp) REVERT: T 2034 LEU cc_start: 0.9417 (tt) cc_final: 0.9180 (pp) REVERT: T 2163 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7873 (p0) REVERT: T 2181 MET cc_start: 0.8304 (mpp) cc_final: 0.8048 (pmm) REVERT: T 2215 LYS cc_start: 0.8726 (mttt) cc_final: 0.8467 (mttt) REVERT: T 2279 MET cc_start: 0.9616 (mmm) cc_final: 0.9246 (mmm) REVERT: T 2305 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8763 (mmm160) REVERT: T 2316 TYR cc_start: 0.8811 (m-80) cc_final: 0.8586 (m-80) REVERT: T 2342 HIS cc_start: 0.9171 (m-70) cc_final: 0.8926 (m-70) REVERT: T 2416 MET cc_start: 0.7612 (mpp) cc_final: 0.6990 (mpp) REVERT: T 2446 ASP cc_start: 0.9013 (t0) cc_final: 0.8713 (t70) REVERT: T 2605 MET cc_start: 0.8106 (mtm) cc_final: 0.7593 (mtm) REVERT: T 2624 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8670 (mmmm) REVERT: T 2731 ASP cc_start: 0.9009 (m-30) cc_final: 0.8671 (t0) REVERT: T 2773 ARG cc_start: 0.9138 (ptm160) cc_final: 0.8624 (ttp80) REVERT: T 2852 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8466 (m-80) REVERT: T 2897 MET cc_start: 0.8344 (ttm) cc_final: 0.8083 (ttm) REVERT: T 2957 HIS cc_start: 0.9520 (OUTLIER) cc_final: 0.9120 (t-90) REVERT: T 2959 MET cc_start: 0.9206 (pmm) cc_final: 0.9001 (pmm) REVERT: T 3022 PHE cc_start: 0.8956 (m-10) cc_final: 0.8564 (m-80) REVERT: T 3093 LYS cc_start: 0.9004 (ptpt) cc_final: 0.8772 (ptpt) REVERT: T 3099 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7795 (tm-30) REVERT: T 3283 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8778 (t80) REVERT: T 3558 MET cc_start: 0.8842 (mtp) cc_final: 0.8555 (mtp) REVERT: T 3562 MET cc_start: 0.9198 (ttp) cc_final: 0.8849 (ptm) REVERT: T 3576 LYS cc_start: 0.9389 (mtmt) cc_final: 0.9085 (mtmm) outliers start: 205 outliers final: 151 residues processed: 633 average time/residue: 0.2200 time to fit residues: 237.3498 Evaluate side-chains 627 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 464 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 171 TYR Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 352 ARG Chi-restraints excluded: chain T residue 354 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 400 HIS Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 739 ILE Chi-restraints excluded: chain T residue 740 LEU Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 948 ILE Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1074 ASN Chi-restraints excluded: chain T residue 1086 VAL Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2026 THR Chi-restraints excluded: chain T residue 2027 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2507 ASN Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2611 SER Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2856 THR Chi-restraints excluded: chain T residue 2900 ASP Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3156 LEU Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3574 VAL Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3720 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 267 optimal weight: 7.9990 chunk 269 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 243 optimal weight: 0.9980 chunk 500 optimal weight: 3.9990 chunk 435 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1754 ASN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1998 ASN ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3119 ASN ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.090887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061392 restraints weight = 171181.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062987 restraints weight = 91581.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064126 restraints weight = 60463.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.065063 restraints weight = 46780.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065677 restraints weight = 38706.117| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41847 Z= 0.177 Angle : 0.769 12.993 56664 Z= 0.381 Chirality : 0.045 0.355 6396 Planarity : 0.005 0.069 7199 Dihedral : 6.035 57.479 5489 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.42 % Favored : 90.56 % Rotamer: Outliers : 4.13 % Allowed : 22.82 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.12), residues: 4978 helix: 0.50 (0.10), residues: 2956 sheet: -1.61 (0.36), residues: 181 loop : -2.90 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T2599 TYR 0.018 0.002 TYR F 584 PHE 0.053 0.002 PHE T1767 TRP 0.043 0.002 TRP T2179 HIS 0.006 0.001 HIS T3497 Details of bonding type rmsd covalent geometry : bond 0.00391 (41845) covalent geometry : angle 0.76894 (56664) hydrogen bonds : bond 0.04221 ( 2230) hydrogen bonds : angle 4.84273 ( 6546) Misc. bond : bond 0.00167 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 495 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9591 (ttm) cc_final: 0.9140 (tmm) REVERT: A 227 MET cc_start: 0.8952 (mmm) cc_final: 0.8641 (mmm) REVERT: A 361 GLU cc_start: 0.9477 (tp30) cc_final: 0.9053 (tp30) REVERT: B 98 LEU cc_start: 0.9569 (mt) cc_final: 0.9098 (mt) REVERT: B 144 THR cc_start: 0.9619 (p) cc_final: 0.9373 (t) REVERT: B 425 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8983 (tpp) REVERT: B 444 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8405 (m170) REVERT: B 459 LEU cc_start: 0.9601 (tp) cc_final: 0.9355 (tp) REVERT: D 36 ARG cc_start: 0.8217 (pmt-80) cc_final: 0.7786 (pmt-80) REVERT: D 285 LEU cc_start: 0.9268 (mt) cc_final: 0.8963 (mt) REVERT: D 536 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.6989 (mmmt) REVERT: D 537 LYS cc_start: 0.8314 (tttt) cc_final: 0.8037 (tttp) REVERT: D 573 ARG cc_start: 0.8533 (ptt90) cc_final: 0.8314 (ptm-80) REVERT: D 609 GLU cc_start: 0.9144 (tp30) cc_final: 0.8600 (tm-30) REVERT: D 622 PHE cc_start: 0.8391 (m-10) cc_final: 0.8107 (m-10) REVERT: D 656 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8584 (tm-30) REVERT: D 689 GLU cc_start: 0.8769 (tp30) cc_final: 0.8528 (tp30) REVERT: E 300 MET cc_start: 0.7864 (mmt) cc_final: 0.7659 (mmt) REVERT: E 302 GLN cc_start: 0.9371 (tp40) cc_final: 0.9050 (tp40) REVERT: F 621 ASP cc_start: 0.8957 (t0) cc_final: 0.8507 (t0) REVERT: F 625 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7179 (pm20) REVERT: F 649 TYR cc_start: 0.9296 (m-80) cc_final: 0.9070 (m-10) REVERT: T 35 MET cc_start: 0.4452 (ptt) cc_final: 0.3887 (ptm) REVERT: T 83 PHE cc_start: 0.8603 (t80) cc_final: 0.8305 (t80) REVERT: T 88 MET cc_start: 0.6774 (tpp) cc_final: 0.6528 (tpp) REVERT: T 218 MET cc_start: 0.3937 (mmm) cc_final: 0.3075 (mmt) REVERT: T 474 ARG cc_start: 0.9641 (tpt90) cc_final: 0.9061 (mmm160) REVERT: T 570 LEU cc_start: 0.8814 (pt) cc_final: 0.8612 (pt) REVERT: T 691 MET cc_start: 0.9229 (mmm) cc_final: 0.8711 (mmm) REVERT: T 711 GLU cc_start: 0.9760 (tp30) cc_final: 0.9433 (tp30) REVERT: T 749 LYS cc_start: 0.8989 (mmtt) cc_final: 0.8620 (tppt) REVERT: T 771 MET cc_start: 0.8612 (mmt) cc_final: 0.8319 (mmt) REVERT: T 775 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8701 (pp) REVERT: T 965 ASP cc_start: 0.8987 (p0) cc_final: 0.8667 (p0) REVERT: T 1084 GLU cc_start: 0.8719 (pp20) cc_final: 0.8395 (pp20) REVERT: T 1130 ASN cc_start: 0.8525 (t0) cc_final: 0.8251 (t0) REVERT: T 1133 LEU cc_start: 0.9080 (tp) cc_final: 0.8583 (tp) REVERT: T 1147 ASP cc_start: 0.9064 (t0) cc_final: 0.8524 (t70) REVERT: T 1246 LYS cc_start: 0.9641 (mtmt) cc_final: 0.9346 (mtpp) REVERT: T 1248 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8105 (p) REVERT: T 1263 LEU cc_start: 0.9825 (OUTLIER) cc_final: 0.9578 (pp) REVERT: T 1266 ASP cc_start: 0.9447 (m-30) cc_final: 0.9220 (m-30) REVERT: T 1326 MET cc_start: 0.9109 (mtp) cc_final: 0.8434 (ppp) REVERT: T 1586 LEU cc_start: 0.9315 (mp) cc_final: 0.8860 (tt) REVERT: T 1615 MET cc_start: 0.6736 (mtp) cc_final: 0.6416 (mtp) REVERT: T 1813 TYR cc_start: 0.9314 (t80) cc_final: 0.8981 (t80) REVERT: T 1842 TRP cc_start: 0.8116 (m100) cc_final: 0.7875 (m100) REVERT: T 1903 GLN cc_start: 0.9600 (tt0) cc_final: 0.9364 (tt0) REVERT: T 1907 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8195 (pp) REVERT: T 1937 GLU cc_start: 0.8633 (mp0) cc_final: 0.8372 (mp0) REVERT: T 1957 MET cc_start: 0.8146 (ptm) cc_final: 0.7731 (ppp) REVERT: T 2163 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7877 (p0) REVERT: T 2181 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.8017 (pmm) REVERT: T 2215 LYS cc_start: 0.8690 (mttt) cc_final: 0.8370 (mtmt) REVERT: T 2279 MET cc_start: 0.9630 (mmm) cc_final: 0.9263 (mmm) REVERT: T 2305 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8676 (mmm160) REVERT: T 2316 TYR cc_start: 0.8803 (m-80) cc_final: 0.8592 (m-80) REVERT: T 2342 HIS cc_start: 0.9160 (m-70) cc_final: 0.8913 (m-70) REVERT: T 2387 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: T 2416 MET cc_start: 0.7491 (mpp) cc_final: 0.6938 (mpp) REVERT: T 2446 ASP cc_start: 0.9035 (t0) cc_final: 0.8710 (t70) REVERT: T 2605 MET cc_start: 0.8026 (mtm) cc_final: 0.7561 (mtm) REVERT: T 2624 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8596 (mmmm) REVERT: T 2773 ARG cc_start: 0.9129 (ptm160) cc_final: 0.8613 (ttp80) REVERT: T 2792 GLN cc_start: 0.9331 (tt0) cc_final: 0.8885 (tt0) REVERT: T 2852 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8367 (m-80) REVERT: T 2897 MET cc_start: 0.8370 (ttm) cc_final: 0.8120 (ttm) REVERT: T 2957 HIS cc_start: 0.9525 (OUTLIER) cc_final: 0.9159 (t-90) REVERT: T 3022 PHE cc_start: 0.8960 (m-10) cc_final: 0.8510 (m-80) REVERT: T 3091 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9260 (tt) REVERT: T 3093 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8792 (ptpt) REVERT: T 3283 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8783 (t80) REVERT: T 3558 MET cc_start: 0.8878 (mtp) cc_final: 0.8564 (mtp) REVERT: T 3562 MET cc_start: 0.9150 (ttp) cc_final: 0.8857 (ptm) REVERT: T 3576 LYS cc_start: 0.9315 (mtmt) cc_final: 0.8992 (mtmm) outliers start: 189 outliers final: 136 residues processed: 640 average time/residue: 0.2180 time to fit residues: 237.0962 Evaluate side-chains 626 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 474 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 316 ASN Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 921 ILE Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1074 ASN Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2026 THR Chi-restraints excluded: chain T residue 2027 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2181 MET Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2387 GLU Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2507 ASN Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2900 ASP Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3084 CYS Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3720 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 399 optimal weight: 3.9990 chunk 382 optimal weight: 0.3980 chunk 335 optimal weight: 9.9990 chunk 363 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 423 optimal weight: 9.9990 chunk 480 optimal weight: 0.0980 chunk 299 optimal weight: 20.0000 chunk 351 optimal weight: 0.4980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 354 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1074 ASN ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.091774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.062488 restraints weight = 170191.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064206 restraints weight = 90941.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.065479 restraints weight = 59791.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066240 restraints weight = 44685.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.066780 restraints weight = 37179.232| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41847 Z= 0.152 Angle : 0.770 16.965 56664 Z= 0.378 Chirality : 0.045 0.348 6396 Planarity : 0.005 0.088 7199 Dihedral : 5.911 59.861 5489 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.08 % Favored : 90.90 % Rotamer: Outliers : 3.72 % Allowed : 23.28 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 4978 helix: 0.58 (0.10), residues: 2948 sheet: -1.49 (0.35), residues: 189 loop : -2.84 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG T 474 TYR 0.022 0.001 TYR T 828 PHE 0.052 0.002 PHE T1767 TRP 0.048 0.002 TRP T2179 HIS 0.005 0.001 HIS T2957 Details of bonding type rmsd covalent geometry : bond 0.00338 (41845) covalent geometry : angle 0.76987 (56664) hydrogen bonds : bond 0.04134 ( 2230) hydrogen bonds : angle 4.76466 ( 6546) Misc. bond : bond 0.00166 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 507 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9361 (tpp) cc_final: 0.9072 (tpp) REVERT: A 190 MET cc_start: 0.9590 (ttm) cc_final: 0.9138 (tmm) REVERT: A 227 MET cc_start: 0.9011 (mmm) cc_final: 0.8719 (mmm) REVERT: A 361 GLU cc_start: 0.9464 (tp30) cc_final: 0.9040 (tp30) REVERT: B 82 ASP cc_start: 0.8812 (m-30) cc_final: 0.8404 (m-30) REVERT: B 98 LEU cc_start: 0.9557 (mt) cc_final: 0.9092 (mt) REVERT: B 144 THR cc_start: 0.9604 (p) cc_final: 0.9363 (t) REVERT: B 425 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8984 (tpp) REVERT: B 444 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.8410 (m170) REVERT: B 459 LEU cc_start: 0.9584 (tp) cc_final: 0.9347 (tp) REVERT: D 36 ARG cc_start: 0.8083 (pmt-80) cc_final: 0.7821 (pmt-80) REVERT: D 285 LEU cc_start: 0.9309 (mt) cc_final: 0.9026 (mt) REVERT: D 536 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7116 (mmmt) REVERT: D 537 LYS cc_start: 0.8347 (tttt) cc_final: 0.8071 (tttp) REVERT: D 573 ARG cc_start: 0.8530 (ptt90) cc_final: 0.8282 (ptm-80) REVERT: D 609 GLU cc_start: 0.9146 (tp30) cc_final: 0.8598 (tm-30) REVERT: D 622 PHE cc_start: 0.8344 (m-10) cc_final: 0.8070 (m-10) REVERT: D 656 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8576 (tm-30) REVERT: D 657 GLU cc_start: 0.9486 (tt0) cc_final: 0.9253 (tt0) REVERT: D 689 GLU cc_start: 0.8777 (tp30) cc_final: 0.8551 (tp30) REVERT: E 274 GLU cc_start: 0.9281 (tp30) cc_final: 0.8875 (tp30) REVERT: E 300 MET cc_start: 0.7854 (mmt) cc_final: 0.7637 (mmt) REVERT: E 302 GLN cc_start: 0.9363 (tp40) cc_final: 0.9054 (tp40) REVERT: F 586 LYS cc_start: 0.7781 (mppt) cc_final: 0.7420 (mmtm) REVERT: F 621 ASP cc_start: 0.8956 (t0) cc_final: 0.8432 (t0) REVERT: F 625 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: T 35 MET cc_start: 0.4693 (ptt) cc_final: 0.4221 (ptm) REVERT: T 83 PHE cc_start: 0.8533 (t80) cc_final: 0.8237 (t80) REVERT: T 88 MET cc_start: 0.6731 (tpp) cc_final: 0.6421 (tpp) REVERT: T 218 MET cc_start: 0.4166 (mmm) cc_final: 0.3255 (mmt) REVERT: T 478 LEU cc_start: 0.9739 (OUTLIER) cc_final: 0.9526 (pp) REVERT: T 591 MET cc_start: 0.9397 (mmt) cc_final: 0.9047 (ttp) REVERT: T 691 MET cc_start: 0.9223 (mmm) cc_final: 0.8725 (mmm) REVERT: T 711 GLU cc_start: 0.9739 (tp30) cc_final: 0.9399 (tp30) REVERT: T 749 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8589 (tppt) REVERT: T 771 MET cc_start: 0.8611 (mmt) cc_final: 0.8301 (tmm) REVERT: T 775 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.7681 (pp) REVERT: T 921 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8763 (tt) REVERT: T 965 ASP cc_start: 0.8976 (p0) cc_final: 0.8655 (p0) REVERT: T 1084 GLU cc_start: 0.8711 (pp20) cc_final: 0.8384 (pp20) REVERT: T 1130 ASN cc_start: 0.8441 (t0) cc_final: 0.8180 (t0) REVERT: T 1133 LEU cc_start: 0.9038 (tp) cc_final: 0.8541 (tp) REVERT: T 1147 ASP cc_start: 0.9048 (t0) cc_final: 0.8496 (t70) REVERT: T 1246 LYS cc_start: 0.9643 (mtmt) cc_final: 0.9409 (mtpp) REVERT: T 1248 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7943 (p) REVERT: T 1263 LEU cc_start: 0.9817 (OUTLIER) cc_final: 0.9569 (pp) REVERT: T 1266 ASP cc_start: 0.9437 (m-30) cc_final: 0.9204 (m-30) REVERT: T 1326 MET cc_start: 0.9085 (mtp) cc_final: 0.8430 (ppp) REVERT: T 1586 LEU cc_start: 0.9317 (mp) cc_final: 0.8861 (tt) REVERT: T 1615 MET cc_start: 0.6702 (mtp) cc_final: 0.6363 (mtp) REVERT: T 1813 TYR cc_start: 0.9304 (t80) cc_final: 0.8986 (t80) REVERT: T 1842 TRP cc_start: 0.8091 (m100) cc_final: 0.7818 (m100) REVERT: T 1903 GLN cc_start: 0.9610 (tt0) cc_final: 0.9370 (tt0) REVERT: T 1907 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8216 (pp) REVERT: T 1937 GLU cc_start: 0.8568 (mp0) cc_final: 0.8331 (mp0) REVERT: T 1957 MET cc_start: 0.8149 (ptm) cc_final: 0.7768 (ppp) REVERT: T 2163 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7897 (p0) REVERT: T 2181 MET cc_start: 0.8276 (mpp) cc_final: 0.8000 (pmm) REVERT: T 2215 LYS cc_start: 0.8698 (mttt) cc_final: 0.8402 (mtmt) REVERT: T 2279 MET cc_start: 0.9621 (mmm) cc_final: 0.9245 (mmm) REVERT: T 2305 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8670 (mmm160) REVERT: T 2316 TYR cc_start: 0.8805 (m-80) cc_final: 0.8594 (m-80) REVERT: T 2342 HIS cc_start: 0.9158 (m-70) cc_final: 0.8917 (m-70) REVERT: T 2387 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: T 2416 MET cc_start: 0.7375 (mpp) cc_final: 0.6869 (mpp) REVERT: T 2446 ASP cc_start: 0.9048 (t0) cc_final: 0.8706 (t70) REVERT: T 2530 MET cc_start: 0.9408 (mmp) cc_final: 0.9185 (mmm) REVERT: T 2605 MET cc_start: 0.7956 (mtm) cc_final: 0.7496 (mtm) REVERT: T 2624 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8517 (mmmm) REVERT: T 2744 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8349 (t0) REVERT: T 2773 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8643 (ttp80) REVERT: T 2792 GLN cc_start: 0.9301 (tt0) cc_final: 0.8661 (tt0) REVERT: T 2852 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8283 (m-80) REVERT: T 2897 MET cc_start: 0.8343 (ttm) cc_final: 0.8081 (ttm) REVERT: T 2957 HIS cc_start: 0.9535 (OUTLIER) cc_final: 0.9119 (t-90) REVERT: T 3022 PHE cc_start: 0.8963 (m-10) cc_final: 0.8514 (m-80) REVERT: T 3034 ARG cc_start: 0.9100 (mmp-170) cc_final: 0.8605 (mmp80) REVERT: T 3091 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9246 (tt) REVERT: T 3093 LYS cc_start: 0.9019 (ptpt) cc_final: 0.8773 (ptpt) REVERT: T 3176 GLU cc_start: 0.8673 (mp0) cc_final: 0.8450 (mm-30) REVERT: T 3283 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8783 (t80) REVERT: T 3558 MET cc_start: 0.8871 (mtp) cc_final: 0.8588 (mtp) REVERT: T 3562 MET cc_start: 0.9140 (ttp) cc_final: 0.8845 (ptm) REVERT: T 3576 LYS cc_start: 0.9287 (mtmt) cc_final: 0.8958 (mtmm) outliers start: 170 outliers final: 130 residues processed: 635 average time/residue: 0.2183 time to fit residues: 235.6952 Evaluate side-chains 633 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 485 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 921 ILE Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2026 THR Chi-restraints excluded: chain T residue 2027 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2387 GLU Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2507 ASN Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2744 ASP Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2900 ASP Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3084 CYS Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3720 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 59 optimal weight: 10.0000 chunk 490 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 chunk 337 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 19 optimal weight: 30.0000 chunk 250 optimal weight: 10.0000 chunk 495 optimal weight: 0.9990 chunk 406 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1060 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1700 ASN T1726 GLN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2521 ASN ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.090476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061608 restraints weight = 171751.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064286 restraints weight = 92061.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065111 restraints weight = 50706.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.065647 restraints weight = 37133.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.065785 restraints weight = 34613.818| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41847 Z= 0.207 Angle : 0.799 19.206 56664 Z= 0.395 Chirality : 0.046 0.343 6396 Planarity : 0.005 0.086 7199 Dihedral : 5.954 58.685 5489 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.86 % Favored : 90.12 % Rotamer: Outliers : 3.81 % Allowed : 23.58 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.12), residues: 4978 helix: 0.56 (0.10), residues: 2951 sheet: -1.45 (0.36), residues: 189 loop : -2.82 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 36 TYR 0.056 0.002 TYR F 649 PHE 0.055 0.002 PHE T1767 TRP 0.049 0.002 TRP T2179 HIS 0.005 0.001 HIS F 580 Details of bonding type rmsd covalent geometry : bond 0.00457 (41845) covalent geometry : angle 0.79914 (56664) hydrogen bonds : bond 0.04211 ( 2230) hydrogen bonds : angle 4.86683 ( 6546) Misc. bond : bond 0.00149 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 490 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.9398 (tpp) cc_final: 0.9116 (tpp) REVERT: A 190 MET cc_start: 0.9588 (ttm) cc_final: 0.9144 (tmm) REVERT: A 227 MET cc_start: 0.9069 (mmm) cc_final: 0.8778 (mmm) REVERT: A 361 GLU cc_start: 0.9454 (tp30) cc_final: 0.9025 (tp30) REVERT: B 82 ASP cc_start: 0.8799 (m-30) cc_final: 0.8395 (m-30) REVERT: B 98 LEU cc_start: 0.9562 (mt) cc_final: 0.9081 (mt) REVERT: B 144 THR cc_start: 0.9625 (p) cc_final: 0.9379 (t) REVERT: B 425 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8965 (tpp) REVERT: B 444 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.8398 (m170) REVERT: B 459 LEU cc_start: 0.9602 (tp) cc_final: 0.9379 (tp) REVERT: D 36 ARG cc_start: 0.8125 (pmt-80) cc_final: 0.7888 (pmt-80) REVERT: D 285 LEU cc_start: 0.9301 (mt) cc_final: 0.9032 (mt) REVERT: D 536 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7222 (mmmt) REVERT: D 537 LYS cc_start: 0.8378 (tttt) cc_final: 0.8094 (tttp) REVERT: D 573 ARG cc_start: 0.8516 (ptt90) cc_final: 0.8314 (ptm-80) REVERT: D 609 GLU cc_start: 0.9162 (tp30) cc_final: 0.8615 (tm-30) REVERT: D 622 PHE cc_start: 0.8358 (m-10) cc_final: 0.8064 (m-10) REVERT: D 656 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8584 (tm-30) REVERT: D 657 GLU cc_start: 0.9463 (tt0) cc_final: 0.9230 (tt0) REVERT: D 689 GLU cc_start: 0.8738 (tp30) cc_final: 0.8491 (tp30) REVERT: E 274 GLU cc_start: 0.9263 (tp30) cc_final: 0.8809 (tp30) REVERT: E 278 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9031 (tt) REVERT: E 302 GLN cc_start: 0.9366 (tp40) cc_final: 0.9031 (tp40) REVERT: F 621 ASP cc_start: 0.8970 (t0) cc_final: 0.8426 (t0) REVERT: F 625 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7324 (pm20) REVERT: T 35 MET cc_start: 0.4969 (ptt) cc_final: 0.4454 (ptm) REVERT: T 83 PHE cc_start: 0.8494 (t80) cc_final: 0.8227 (t80) REVERT: T 218 MET cc_start: 0.4676 (mmm) cc_final: 0.3822 (mmt) REVERT: T 691 MET cc_start: 0.9233 (mmm) cc_final: 0.8744 (mmm) REVERT: T 711 GLU cc_start: 0.9727 (tp30) cc_final: 0.9378 (tp30) REVERT: T 749 LYS cc_start: 0.8993 (mmtt) cc_final: 0.8617 (tppt) REVERT: T 771 MET cc_start: 0.8579 (mmt) cc_final: 0.8287 (tmm) REVERT: T 775 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.7770 (pp) REVERT: T 965 ASP cc_start: 0.8963 (p0) cc_final: 0.8642 (p0) REVERT: T 1070 ARG cc_start: 0.8990 (tmm-80) cc_final: 0.8742 (ttp80) REVERT: T 1084 GLU cc_start: 0.8722 (pp20) cc_final: 0.8403 (pp20) REVERT: T 1130 ASN cc_start: 0.8447 (t0) cc_final: 0.8197 (t0) REVERT: T 1133 LEU cc_start: 0.9096 (tp) cc_final: 0.8599 (tp) REVERT: T 1147 ASP cc_start: 0.9061 (t0) cc_final: 0.8517 (t70) REVERT: T 1246 LYS cc_start: 0.9642 (mtmt) cc_final: 0.9408 (mtpp) REVERT: T 1248 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7927 (p) REVERT: T 1263 LEU cc_start: 0.9820 (OUTLIER) cc_final: 0.9571 (pp) REVERT: T 1266 ASP cc_start: 0.9409 (m-30) cc_final: 0.9169 (m-30) REVERT: T 1326 MET cc_start: 0.9071 (mtp) cc_final: 0.8479 (ppp) REVERT: T 1586 LEU cc_start: 0.9317 (mp) cc_final: 0.8860 (tt) REVERT: T 1615 MET cc_start: 0.6653 (mtp) cc_final: 0.6294 (mtp) REVERT: T 1698 MET cc_start: 0.9331 (ppp) cc_final: 0.9093 (ppp) REVERT: T 1813 TYR cc_start: 0.9317 (t80) cc_final: 0.8991 (t80) REVERT: T 1842 TRP cc_start: 0.8116 (m100) cc_final: 0.7859 (m100) REVERT: T 1903 GLN cc_start: 0.9611 (tt0) cc_final: 0.9394 (tt0) REVERT: T 1907 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8177 (pp) REVERT: T 1937 GLU cc_start: 0.8540 (mp0) cc_final: 0.8293 (mp0) REVERT: T 1957 MET cc_start: 0.8132 (ptm) cc_final: 0.7742 (ppp) REVERT: T 2038 TRP cc_start: 0.6443 (t60) cc_final: 0.6242 (t60) REVERT: T 2163 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7925 (p0) REVERT: T 2181 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8020 (pmm) REVERT: T 2215 LYS cc_start: 0.8746 (mttt) cc_final: 0.8540 (mttt) REVERT: T 2279 MET cc_start: 0.9612 (mmm) cc_final: 0.9265 (mmm) REVERT: T 2305 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8722 (mmm160) REVERT: T 2342 HIS cc_start: 0.9127 (m-70) cc_final: 0.8883 (m-70) REVERT: T 2416 MET cc_start: 0.7455 (mpp) cc_final: 0.6887 (mpp) REVERT: T 2446 ASP cc_start: 0.8996 (t0) cc_final: 0.8670 (t70) REVERT: T 2530 MET cc_start: 0.9391 (mmp) cc_final: 0.9162 (mmm) REVERT: T 2605 MET cc_start: 0.8015 (mtm) cc_final: 0.7491 (mtm) REVERT: T 2624 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8583 (mmmm) REVERT: T 2744 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8421 (t0) REVERT: T 2773 ARG cc_start: 0.9109 (ptm160) cc_final: 0.8619 (ttp80) REVERT: T 2852 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: T 2897 MET cc_start: 0.8336 (ttm) cc_final: 0.8089 (ttm) REVERT: T 2957 HIS cc_start: 0.9509 (OUTLIER) cc_final: 0.9114 (t-90) REVERT: T 3022 PHE cc_start: 0.8984 (m-10) cc_final: 0.8521 (m-80) REVERT: T 3034 ARG cc_start: 0.9093 (mmp-170) cc_final: 0.8632 (mmp80) REVERT: T 3091 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9272 (tt) REVERT: T 3093 LYS cc_start: 0.9008 (ptpt) cc_final: 0.8773 (ptpt) REVERT: T 3176 GLU cc_start: 0.8656 (mp0) cc_final: 0.8456 (mm-30) REVERT: T 3283 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8785 (t80) REVERT: T 3558 MET cc_start: 0.8899 (mtp) cc_final: 0.8605 (mtp) REVERT: T 3562 MET cc_start: 0.9194 (ttp) cc_final: 0.8848 (ptm) REVERT: T 3576 LYS cc_start: 0.9329 (mtmt) cc_final: 0.8994 (mtmm) outliers start: 174 outliers final: 142 residues processed: 622 average time/residue: 0.2192 time to fit residues: 231.4705 Evaluate side-chains 638 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 479 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 124 THR Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 478 LEU Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1726 GLN Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2026 THR Chi-restraints excluded: chain T residue 2027 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2181 MET Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2744 ASP Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2900 ASP Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3084 CYS Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3241 THR Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3720 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 21 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 368 optimal weight: 0.0010 chunk 70 optimal weight: 0.9980 chunk 389 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 433 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** D 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1726 GLN ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1987 GLN ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3119 ASN ** T3250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.092842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064013 restraints weight = 169071.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.065699 restraints weight = 94704.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066827 restraints weight = 61815.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.068118 restraints weight = 42885.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068165 restraints weight = 34212.653| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41847 Z= 0.145 Angle : 0.805 20.204 56664 Z= 0.392 Chirality : 0.046 0.425 6396 Planarity : 0.005 0.091 7199 Dihedral : 5.822 57.873 5489 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.54 % Favored : 91.44 % Rotamer: Outliers : 3.02 % Allowed : 24.33 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.12), residues: 4978 helix: 0.59 (0.10), residues: 2953 sheet: -1.27 (0.36), residues: 187 loop : -2.75 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 474 TYR 0.049 0.001 TYR T2316 PHE 0.070 0.002 PHE T2235 TRP 0.053 0.002 TRP T2179 HIS 0.006 0.001 HIS D 675 Details of bonding type rmsd covalent geometry : bond 0.00318 (41845) covalent geometry : angle 0.80478 (56664) hydrogen bonds : bond 0.04084 ( 2230) hydrogen bonds : angle 4.72907 ( 6546) Misc. bond : bond 0.00184 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 526 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9587 (ttm) cc_final: 0.9128 (tmm) REVERT: A 227 MET cc_start: 0.9084 (mmm) cc_final: 0.8798 (mmm) REVERT: A 361 GLU cc_start: 0.9461 (tp30) cc_final: 0.9015 (tp30) REVERT: B 82 ASP cc_start: 0.8803 (m-30) cc_final: 0.8386 (m-30) REVERT: B 98 LEU cc_start: 0.9546 (mt) cc_final: 0.9099 (mt) REVERT: B 144 THR cc_start: 0.9569 (p) cc_final: 0.9323 (t) REVERT: B 425 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.8932 (tpp) REVERT: B 444 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8345 (m170) REVERT: B 459 LEU cc_start: 0.9569 (tp) cc_final: 0.9334 (tp) REVERT: D 36 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7778 (pmt-80) REVERT: D 285 LEU cc_start: 0.9287 (mt) cc_final: 0.9029 (mt) REVERT: D 536 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7260 (mmmt) REVERT: D 537 LYS cc_start: 0.8321 (tttt) cc_final: 0.8060 (tttp) REVERT: D 609 GLU cc_start: 0.9142 (tp30) cc_final: 0.8580 (tm-30) REVERT: D 656 GLN cc_start: 0.9110 (tp-100) cc_final: 0.8620 (tm-30) REVERT: D 657 GLU cc_start: 0.9479 (tt0) cc_final: 0.9218 (tt0) REVERT: D 689 GLU cc_start: 0.8750 (tp30) cc_final: 0.8520 (tp30) REVERT: E 235 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8684 (mm-30) REVERT: E 274 GLU cc_start: 0.9220 (tp30) cc_final: 0.8836 (tp30) REVERT: E 278 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9021 (tt) REVERT: E 302 GLN cc_start: 0.9372 (tp40) cc_final: 0.9044 (tp40) REVERT: F 586 LYS cc_start: 0.7743 (mppt) cc_final: 0.7367 (mmtm) REVERT: F 621 ASP cc_start: 0.8934 (t0) cc_final: 0.8367 (t0) REVERT: F 625 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7310 (pm20) REVERT: T 35 MET cc_start: 0.5038 (ptt) cc_final: 0.4670 (ptt) REVERT: T 83 PHE cc_start: 0.8511 (t80) cc_final: 0.8262 (t80) REVERT: T 88 MET cc_start: 0.6500 (tpp) cc_final: 0.6202 (tpp) REVERT: T 119 MET cc_start: 0.0496 (mtp) cc_final: 0.0226 (mtp) REVERT: T 218 MET cc_start: 0.4305 (mmm) cc_final: 0.3990 (mmt) REVERT: T 570 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8647 (pt) REVERT: T 591 MET cc_start: 0.9286 (mmt) cc_final: 0.9067 (ttp) REVERT: T 691 MET cc_start: 0.9212 (mmm) cc_final: 0.8740 (mmm) REVERT: T 711 GLU cc_start: 0.9725 (tp30) cc_final: 0.9374 (tp30) REVERT: T 749 LYS cc_start: 0.8972 (mmtt) cc_final: 0.8587 (tppt) REVERT: T 771 MET cc_start: 0.8522 (mmt) cc_final: 0.8246 (tmm) REVERT: T 775 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.7693 (pp) REVERT: T 965 ASP cc_start: 0.8979 (p0) cc_final: 0.8659 (p0) REVERT: T 979 ASP cc_start: 0.8982 (p0) cc_final: 0.8531 (t0) REVERT: T 1084 GLU cc_start: 0.8674 (pp20) cc_final: 0.8345 (pp20) REVERT: T 1133 LEU cc_start: 0.9014 (tp) cc_final: 0.8510 (tp) REVERT: T 1147 ASP cc_start: 0.9031 (t0) cc_final: 0.8436 (t70) REVERT: T 1246 LYS cc_start: 0.9622 (mtmt) cc_final: 0.9392 (mtpp) REVERT: T 1248 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7785 (p) REVERT: T 1251 GLU cc_start: 0.7218 (pm20) cc_final: 0.6899 (pm20) REVERT: T 1263 LEU cc_start: 0.9815 (OUTLIER) cc_final: 0.9569 (pp) REVERT: T 1266 ASP cc_start: 0.9428 (m-30) cc_final: 0.9192 (m-30) REVERT: T 1326 MET cc_start: 0.9069 (mtp) cc_final: 0.8512 (ppp) REVERT: T 1568 MET cc_start: 0.8363 (tmm) cc_final: 0.8036 (tmm) REVERT: T 1586 LEU cc_start: 0.9309 (mp) cc_final: 0.8902 (tt) REVERT: T 1615 MET cc_start: 0.6554 (mtp) cc_final: 0.6221 (mtp) REVERT: T 1728 LEU cc_start: 0.9557 (tp) cc_final: 0.9279 (pp) REVERT: T 1813 TYR cc_start: 0.9298 (t80) cc_final: 0.8997 (t80) REVERT: T 1842 TRP cc_start: 0.8120 (m100) cc_final: 0.7817 (m100) REVERT: T 1903 GLN cc_start: 0.9610 (tt0) cc_final: 0.9357 (tt0) REVERT: T 1907 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8257 (pp) REVERT: T 1957 MET cc_start: 0.8144 (ptm) cc_final: 0.7749 (ppp) REVERT: T 2163 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7944 (p0) REVERT: T 2181 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8001 (pmm) REVERT: T 2214 MET cc_start: 0.8953 (tmm) cc_final: 0.8743 (tmm) REVERT: T 2215 LYS cc_start: 0.8709 (mttt) cc_final: 0.8333 (mtmt) REVERT: T 2279 MET cc_start: 0.9619 (mmm) cc_final: 0.9246 (mmm) REVERT: T 2305 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8718 (mmm160) REVERT: T 2342 HIS cc_start: 0.9126 (m-70) cc_final: 0.8902 (m-70) REVERT: T 2387 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8131 (mp0) REVERT: T 2416 MET cc_start: 0.7325 (mpp) cc_final: 0.6873 (mpp) REVERT: T 2446 ASP cc_start: 0.9014 (t0) cc_final: 0.8666 (t70) REVERT: T 2530 MET cc_start: 0.9421 (mmp) cc_final: 0.9185 (mmm) REVERT: T 2605 MET cc_start: 0.7830 (mtm) cc_final: 0.7364 (mtm) REVERT: T 2624 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8464 (mmmm) REVERT: T 2773 ARG cc_start: 0.9101 (ptm160) cc_final: 0.8626 (ttp80) REVERT: T 2792 GLN cc_start: 0.9286 (tt0) cc_final: 0.8829 (tt0) REVERT: T 2793 MET cc_start: 0.9078 (ttp) cc_final: 0.8427 (ppp) REVERT: T 2852 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: T 2896 ASN cc_start: 0.9010 (t0) cc_final: 0.8773 (t0) REVERT: T 2897 MET cc_start: 0.8276 (ttm) cc_final: 0.8003 (ttm) REVERT: T 2957 HIS cc_start: 0.9518 (OUTLIER) cc_final: 0.9138 (t-90) REVERT: T 3022 PHE cc_start: 0.8991 (m-10) cc_final: 0.8566 (m-80) REVERT: T 3034 ARG cc_start: 0.9093 (mmp-170) cc_final: 0.8600 (mmp80) REVERT: T 3091 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9253 (tt) REVERT: T 3093 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8753 (ptpt) REVERT: T 3176 GLU cc_start: 0.8636 (mp0) cc_final: 0.8427 (mm-30) REVERT: T 3248 LEU cc_start: 0.9756 (tp) cc_final: 0.9372 (tt) REVERT: T 3350 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6608 (tm-30) REVERT: T 3558 MET cc_start: 0.8839 (mtp) cc_final: 0.8585 (mtp) REVERT: T 3562 MET cc_start: 0.9083 (ttp) cc_final: 0.8862 (ptm) REVERT: T 3576 LYS cc_start: 0.9248 (mtmt) cc_final: 0.8911 (mtmm) outliers start: 138 outliers final: 112 residues processed: 627 average time/residue: 0.2163 time to fit residues: 229.8804 Evaluate side-chains 620 residues out of total 4598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 490 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 570 LEU Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1726 GLN Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1907 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2027 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2181 MET Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2387 GLU Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2900 ASP Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3084 CYS Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3241 THR Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3505 ASP Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3720 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 31 optimal weight: 10.0000 chunk 421 optimal weight: 0.0020 chunk 239 optimal weight: 0.0570 chunk 162 optimal weight: 0.0060 chunk 351 optimal weight: 9.9990 chunk 320 optimal weight: 30.0000 chunk 447 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 412 optimal weight: 4.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** D 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1726 GLN ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.091944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063539 restraints weight = 172718.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.064785 restraints weight = 98361.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066412 restraints weight = 68082.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066590 restraints weight = 43239.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066730 restraints weight = 41600.002| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 41847 Z= 0.167 Angle : 0.810 20.045 56664 Z= 0.398 Chirality : 0.046 0.340 6396 Planarity : 0.005 0.089 7199 Dihedral : 5.797 57.987 5489 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.02 % Favored : 90.96 % Rotamer: Outliers : 3.13 % Allowed : 24.59 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.12), residues: 4978 helix: 0.62 (0.10), residues: 2958 sheet: -1.25 (0.38), residues: 177 loop : -2.75 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T1618 TYR 0.063 0.002 TYR T2316 PHE 0.057 0.002 PHE T1767 TRP 0.054 0.002 TRP T2179 HIS 0.005 0.001 HIS T1935 Details of bonding type rmsd covalent geometry : bond 0.00375 (41845) covalent geometry : angle 0.80998 (56664) hydrogen bonds : bond 0.04092 ( 2230) hydrogen bonds : angle 4.76817 ( 6546) Misc. bond : bond 0.00148 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7838.06 seconds wall clock time: 136 minutes 36.11 seconds (8196.11 seconds total)