Starting phenix.real_space_refine on Sun Jul 5 20:11:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4e_24148/07_2026/7n4e_24148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4e_24148/07_2026/7n4e_24148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n4e_24148/07_2026/7n4e_24148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4e_24148/07_2026/7n4e_24148_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n4e_24148/07_2026/7n4e_24148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4e_24148/07_2026/7n4e_24148.map" } resolution = 3.8 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 89 5.49 5 Mg 1 5.21 5 S 125 5.16 5 C 18412 2.51 5 N 5284 2.21 5 O 5909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29822 Number of models: 1 Model: "" Number of chains: 10 Chain: "1" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 785 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "2" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 830 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain breaks: 1 Chain: "A" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10568 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10319 Classifications: {'peptide': 1327} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1271} Chain breaks: 2 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "F" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2943 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 9, 'TRANS': 349} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16208 SG CYS D 72 98.609 126.868 120.725 1.00 98.14 S ATOM 22665 SG CYS D 898 103.092 62.630 90.623 1.00 47.28 S Time building chain proxies: 5.96, per 1000 atoms: 0.20 Number of scatterers: 29822 At special positions: 0 Unit cell: (144.48, 159.6, 198.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 125 16.00 P 89 15.00 Mg 1 11.99 O 5909 8.00 N 5284 7.00 C 18412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6598 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 45 sheets defined 43.4% alpha, 14.7% beta 26 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.892A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.055A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.853A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.728A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.892A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 4.056A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.854A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 233 removed outlier: 3.728A pdb=" N ALA B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.704A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.764A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 346 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.992A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.861A pdb=" N MET C 492 " --> pdb=" O PRO C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 544 through 549 removed outlier: 3.724A pdb=" N ARG C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP C 549 " --> pdb=" O PHE C 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 544 through 549' Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.645A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.919A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.671A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 902 removed outlier: 4.123A pdb=" N LEU C 902 " --> pdb=" O GLU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 905 No H-bonds generated for 'chain 'C' and resid 903 through 905' Processing helix chain 'C' and resid 942 through 983 Processing helix chain 'C' and resid 986 through 991 removed outlier: 3.986A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 3.995A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1135 Processing helix chain 'C' and resid 1138 through 1150 Processing helix chain 'C' and resid 1165 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.614A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.650A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.634A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 286 removed outlier: 3.903A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.608A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.537A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.744A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.591A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.829A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.610A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.557A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.077A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1063 through 1067 removed outlier: 3.565A pdb=" N ARG D1067 " --> pdb=" O SER D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.688A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.548A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.346A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1360 through 1375 removed outlier: 4.484A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 60 through 76 removed outlier: 3.507A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 114 through 136 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 157 through 161 removed outlier: 4.275A pdb=" N LEU F 161 " --> pdb=" O ARG F 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 161' Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 237 through 237 No H-bonds generated for 'chain 'F' and resid 237 through 237' Processing helix chain 'F' and resid 243 through 256 Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.528A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.237A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 322 Processing helix chain 'F' and resid 327 through 332 removed outlier: 3.641A pdb=" N HIS F 331 " --> pdb=" O GLU F 328 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP F 332 " --> pdb=" O LYS F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 352 Processing helix chain 'F' and resid 354 through 382 Processing helix chain 'F' and resid 383 through 392 removed outlier: 3.632A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 400 through 419 Processing helix chain 'F' and resid 420 through 424 removed outlier: 4.031A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 447 removed outlier: 3.821A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP F 445 " --> pdb=" O ARG F 441 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F 447 " --> pdb=" O ILE F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 4.110A pdb=" N ILE F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 4.185A pdb=" N LEU F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.811A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 104 removed outlier: 7.220A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.499A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.811A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 104 removed outlier: 7.220A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.499A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.514A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.835A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 96 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLU C 106 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LYS C 115 " --> pdb=" O GLU C 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.502A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 160 removed outlier: 3.786A pdb=" N LEU C 171 " --> pdb=" O ASP C 160 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N TYR C 172 " --> pdb=" O PHE C 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 287 removed outlier: 4.208A pdb=" N LEU C 237 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.947A pdb=" N CYS C 311 " --> pdb=" O TYR C 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.753A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.753A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.957A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC5, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.498A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.990A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.750A pdb=" N THR C 888 " --> pdb=" O LYS C 914 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.811A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.224A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1340 Processing sheet with id=AD5, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.796A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.520A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 5.184A pdb=" N VAL D 146 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS D 179 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 148 " --> pdb=" O ASP D 177 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.834A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 547 through 557 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 958 through 961 removed outlier: 6.710A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 965 through 966 removed outlier: 3.724A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AE5, first strand: chain 'D' and resid 1046 through 1050 removed outlier: 3.917A pdb=" N VAL D1060 " --> pdb=" O THR D1047 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN D1049 " --> pdb=" O SER D1058 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D1058 " --> pdb=" O GLN D1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1161 through 1162 Processing sheet with id=AE7, first strand: chain 'D' and resid 1164 through 1167 removed outlier: 6.776A pdb=" N ARG D1174 " --> pdb=" O GLY D1166 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 3.582A pdb=" N VAL D1280 " --> pdb=" O ALA D1264 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D1267 " --> pdb=" O THR D1301 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 162 through 164 removed outlier: 7.075A pdb=" N ARG F 260 " --> pdb=" O THR F 163 " (cutoff:3.500A) 1269 hydrogen bonds defined for protein. 3624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 7.74 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9550 1.34 - 1.46: 4396 1.46 - 1.58: 16111 1.58 - 1.70: 172 1.70 - 1.82: 219 Bond restraints: 30448 Sorted by residual: bond pdb=" O3' DT 1 59 " pdb=" P DA 1 60 " ideal model delta sigma weight residual 1.607 1.501 0.106 1.50e-02 4.44e+03 4.98e+01 bond pdb=" C1' DG 1 27 " pdb=" N9 DG 1 27 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.41e+01 bond pdb=" C1' DT 1 26 " pdb=" N1 DT 1 26 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.38e+01 bond pdb=" C1' DT 1 20 " pdb=" N1 DT 1 20 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.36e+01 bond pdb=" C1' DT 2 40 " pdb=" N1 DT 2 40 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.30e+01 ... (remaining 30443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 41137 2.95 - 5.90: 303 5.90 - 8.86: 33 8.86 - 11.81: 4 11.81 - 14.76: 4 Bond angle restraints: 41481 Sorted by residual: angle pdb=" C3' DT 1 59 " pdb=" O3' DT 1 59 " pdb=" P DA 1 60 " ideal model delta sigma weight residual 120.20 134.23 -14.03 1.50e+00 4.44e-01 8.75e+01 angle pdb=" C MET D 822 " pdb=" N THR D 823 " pdb=" CA THR D 823 " ideal model delta sigma weight residual 122.36 137.12 -14.76 2.42e+00 1.71e-01 3.72e+01 angle pdb=" CB ARG A 191 " pdb=" CG ARG A 191 " pdb=" CD ARG A 191 " ideal model delta sigma weight residual 111.30 123.80 -12.50 2.30e+00 1.89e-01 2.95e+01 angle pdb=" CB ARG B 191 " pdb=" CG ARG B 191 " pdb=" CD ARG B 191 " ideal model delta sigma weight residual 111.30 123.77 -12.47 2.30e+00 1.89e-01 2.94e+01 angle pdb=" N VAL D 706 " pdb=" CA VAL D 706 " pdb=" C VAL D 706 " ideal model delta sigma weight residual 113.43 107.69 5.74 1.09e+00 8.42e-01 2.78e+01 ... (remaining 41476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 17597 33.19 - 66.38: 928 66.38 - 99.57: 54 99.57 - 132.76: 0 132.76 - 165.95: 1 Dihedral angle restraints: 18580 sinusoidal: 8338 harmonic: 10242 Sorted by residual: dihedral pdb=" CG ARG B 45 " pdb=" CD ARG B 45 " pdb=" NE ARG B 45 " pdb=" CZ ARG B 45 " ideal model delta sinusoidal sigma weight residual 90.00 6.03 83.97 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" CG ARG A 45 " pdb=" CD ARG A 45 " pdb=" NE ARG A 45 " pdb=" CZ ARG A 45 " ideal model delta sinusoidal sigma weight residual 90.00 6.05 83.95 2 1.50e+01 4.44e-03 2.11e+01 dihedral pdb=" CA GLU A 97 " pdb=" C GLU A 97 " pdb=" N VAL A 98 " pdb=" CA VAL A 98 " ideal model delta harmonic sigma weight residual 180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 18577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 4284 0.078 - 0.157: 426 0.157 - 0.235: 13 0.235 - 0.314: 1 0.314 - 0.392: 1 Chirality restraints: 4725 Sorted by residual: chirality pdb=" C3' DT 2 2 " pdb=" C4' DT 2 2 " pdb=" O3' DT 2 2 " pdb=" C2' DT 2 2 " both_signs ideal model delta sigma weight residual False -2.73 -2.34 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CB ILE D1106 " pdb=" CA ILE D1106 " pdb=" CG1 ILE D1106 " pdb=" CG2 ILE D1106 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS D 321 " pdb=" N LYS D 321 " pdb=" C LYS D 321 " pdb=" CB LYS D 321 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 4722 not shown) Planarity restraints: 5115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 45 " 0.382 9.50e-02 1.11e+02 1.72e-01 1.96e+01 pdb=" NE ARG A 45 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 45 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 45 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 45 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 45 " 0.382 9.50e-02 1.11e+02 1.71e-01 1.95e+01 pdb=" NE ARG B 45 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG B 45 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 45 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 45 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 55 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.14e+00 pdb=" CD GLU E 55 " 0.049 2.00e-02 2.50e+03 pdb=" OE1 GLU E 55 " -0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU E 55 " -0.018 2.00e-02 2.50e+03 ... (remaining 5112 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 64 2.34 - 2.98: 14570 2.98 - 3.62: 44443 3.62 - 4.26: 66245 4.26 - 4.90: 109371 Nonbonded interactions: 234693 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb=" OD2 ASP D 464 " model vdw 1.705 3.040 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1501 " model vdw 2.020 2.310 nonbonded pdb=" O SER D 884 " pdb="ZN ZN D1502 " model vdw 2.037 2.230 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.050 2.170 nonbonded pdb=" O ARG C 542 " pdb=" NE ARG C 542 " model vdw 2.077 3.120 ... (remaining 234688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 233) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 34.550 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.004 0.106 30450 Z= 0.254 Angle : 0.726 14.761 41481 Z= 0.443 Chirality : 0.046 0.392 4725 Planarity : 0.005 0.172 5115 Dihedral : 17.756 165.952 11982 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.45 % Allowed : 1.22 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.65 (0.14), residues: 3539 helix: 0.73 (0.14), residues: 1404 sheet: -0.18 (0.27), residues: 353 loop : -1.47 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 45 TYR 0.015 0.001 TYR D 679 PHE 0.016 0.001 PHE B 231 TRP 0.043 0.002 TRP D 33 HIS 0.004 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.25 (30448) covalent geometry : angle 0.72601 / 0.44 (41481) hydrogen bonds : bond 0.14402 / 16.14 ( 1331) hydrogen bonds : angle 6.02335 / 6.60 ( 3750) metal coordination : bond 0.00454 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 254 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 125 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6976 (ttpp) REVERT: A 159 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7972 (mm) REVERT: A 229 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5805 (tm-30) REVERT: B 54 CYS cc_start: 0.6443 (OUTLIER) cc_final: 0.4404 (m) REVERT: B 78 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8406 (pt) REVERT: B 81 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.7066 (mm) REVERT: B 107 ILE cc_start: 0.5896 (mm) cc_final: 0.5503 (tp) REVERT: B 144 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7100 (mp) REVERT: B 194 GLN cc_start: 0.2167 (OUTLIER) cc_final: 0.1735 (tt0) REVERT: B 224 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7743 (mt) REVERT: C 185 ASP cc_start: 0.8001 (t70) cc_final: 0.7546 (t0) REVERT: C 492 MET cc_start: 0.8069 (mpp) cc_final: 0.7846 (mpp) REVERT: C 1275 VAL cc_start: 0.8508 (t) cc_final: 0.8252 (t) REVERT: C 1304 MET cc_start: 0.7064 (tpp) cc_final: 0.6685 (tpp) REVERT: E 41 GLU cc_start: 0.7869 (pp20) cc_final: 0.7621 (pp20) REVERT: E 67 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8062 (tpp-160) REVERT: E 71 GLU cc_start: 0.9077 (tt0) cc_final: 0.8469 (tm-30) REVERT: F 101 TYR cc_start: 0.9189 (t80) cc_final: 0.8939 (t80) outliers start: 106 outliers final: 17 residues processed: 337 average time/residue: 0.2061 time to fit residues: 111.2134 Evaluate side-chains 226 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 GLN Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 480 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0070 chunk 298 optimal weight: 30.0000 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS B 18 GLN B 37 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN D 200 GLN D 341 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS E 75 GLN F 362 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.124210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094904 restraints weight = 74768.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093611 restraints weight = 65058.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094635 restraints weight = 59242.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094693 restraints weight = 45499.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095239 restraints weight = 40022.121| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30450 Z= 0.133 Angle : 0.599 10.690 41481 Z= 0.320 Chirality : 0.044 0.212 4725 Planarity : 0.004 0.046 5115 Dihedral : 15.688 150.618 4997 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.74 % Allowed : 8.22 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.36 (0.14), residues: 3539 helix: 0.97 (0.14), residues: 1436 sheet: -0.23 (0.26), residues: 372 loop : -1.30 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 182 TYR 0.032 0.001 TYR D 165 PHE 0.016 0.001 PHE B 231 TRP 0.024 0.001 TRP D 33 HIS 0.006 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (30448) covalent geometry : angle 0.59887 / 0.32 (41481) hydrogen bonds : bond 0.04719 / 5.27 ( 1331) hydrogen bonds : angle 4.77645 / 5.28 ( 3750) metal coordination : bond 0.00200 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 1.063 Fit side-chains revert: symmetry clash Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 159 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 229 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5747 (tm-30) REVERT: B 71 LYS cc_start: 0.6868 (tptp) cc_final: 0.6522 (tptp) REVERT: B 78 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8358 (tp) REVERT: B 107 ILE cc_start: 0.6041 (mm) cc_final: 0.5635 (tp) REVERT: B 194 GLN cc_start: 0.0782 (OUTLIER) cc_final: -0.0006 (tt0) REVERT: B 224 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8017 (mt) REVERT: C 185 ASP cc_start: 0.8076 (t70) cc_final: 0.7484 (t0) REVERT: C 237 LEU cc_start: 0.6853 (mt) cc_final: 0.6592 (mt) REVERT: C 315 MET cc_start: 0.5627 (ppp) cc_final: 0.4767 (ppp) REVERT: C 951 MET cc_start: 0.8212 (mmm) cc_final: 0.7877 (mmm) REVERT: C 1085 MET cc_start: 0.9144 (mmm) cc_final: 0.8937 (mmm) REVERT: C 1290 MET cc_start: 0.8211 (mtt) cc_final: 0.8000 (mtt) REVERT: D 140 TYR cc_start: 0.8043 (m-10) cc_final: 0.7535 (m-10) REVERT: D 525 MET cc_start: 0.6081 (tpp) cc_final: 0.5655 (mmm) REVERT: D 527 LEU cc_start: 0.8284 (mt) cc_final: 0.7911 (mt) REVERT: D 869 CYS cc_start: 0.8608 (t) cc_final: 0.8156 (t) REVERT: D 1095 MET cc_start: 0.4433 (mmt) cc_final: 0.4068 (ptm) REVERT: E 67 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8017 (tpp-160) REVERT: E 69 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8190 (tpp80) REVERT: E 70 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7773 (tm-30) REVERT: E 71 GLU cc_start: 0.8988 (tt0) cc_final: 0.8470 (tm-30) outliers start: 54 outliers final: 30 residues processed: 268 average time/residue: 0.1791 time to fit residues: 79.8904 Evaluate side-chains 235 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1281 TYR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 467 SER Chi-restraints excluded: chain F residue 480 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 213 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 218 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN C1313 HIS D 200 GLN D 716 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN ** D1126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 227 GLN F 265 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.114532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085513 restraints weight = 74725.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.083490 restraints weight = 68473.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084540 restraints weight = 70995.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.084481 restraints weight = 50961.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.085020 restraints weight = 43920.141| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30450 Z= 0.235 Angle : 0.727 9.612 41481 Z= 0.387 Chirality : 0.047 0.198 4725 Planarity : 0.005 0.051 5115 Dihedral : 15.283 135.028 4960 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.73 % Allowed : 12.20 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.52 (0.14), residues: 3539 helix: 0.82 (0.14), residues: 1431 sheet: -0.25 (0.27), residues: 352 loop : -1.36 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 191 TYR 0.028 0.002 TYR F 148 PHE 0.025 0.002 PHE D1145 TRP 0.031 0.002 TRP D 33 HIS 0.008 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (30448) covalent geometry : angle 0.72741 / 0.39 (41481) hydrogen bonds : bond 0.05650 / 6.37 ( 1331) hydrogen bonds : angle 4.75542 / 5.25 ( 3750) metal coordination : bond 0.00150 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 210 time to evaluate : 1.059 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6105 (pm20) REVERT: A 187 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.7553 (m) REVERT: A 200 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7883 (ptmt) REVERT: A 229 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6561 (tp30) REVERT: B 78 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8576 (tp) REVERT: B 104 LYS cc_start: 0.6117 (mmtm) cc_final: 0.5882 (mmtm) REVERT: B 107 ILE cc_start: 0.6103 (mm) cc_final: 0.5756 (tp) REVERT: B 194 GLN cc_start: 0.0986 (OUTLIER) cc_final: 0.0186 (tt0) REVERT: B 207 THR cc_start: 0.6293 (OUTLIER) cc_final: 0.6068 (t) REVERT: B 224 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8294 (mm) REVERT: C 185 ASP cc_start: 0.8494 (t70) cc_final: 0.7785 (t0) REVERT: C 194 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7951 (pp) REVERT: C 315 MET cc_start: 0.5556 (ppp) cc_final: 0.5319 (ppp) REVERT: C 1010 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7407 (tp40) REVERT: C 1315 MET cc_start: 0.7478 (ptp) cc_final: 0.7239 (ptt) REVERT: D 165 TYR cc_start: 0.7458 (t80) cc_final: 0.6747 (t80) REVERT: D 197 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7204 (tt0) REVERT: D 743 MET cc_start: 0.8286 (ttt) cc_final: 0.8081 (ttt) REVERT: D 869 CYS cc_start: 0.8630 (t) cc_final: 0.8295 (t) REVERT: D 1040 MET cc_start: 0.5531 (pmm) cc_final: 0.5205 (pmm) REVERT: D 1095 MET cc_start: 0.4578 (mmt) cc_final: 0.4105 (ptm) REVERT: D 1189 MET cc_start: 0.7535 (tmm) cc_final: 0.7333 (tmm) REVERT: D 1273 ASP cc_start: 0.6882 (t0) cc_final: 0.6635 (t0) REVERT: E 15 ASN cc_start: 0.6836 (t0) cc_final: 0.6399 (t0) REVERT: E 69 ARG cc_start: 0.8408 (tpp80) cc_final: 0.8205 (tpp80) REVERT: E 70 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7095 (tm-30) REVERT: E 71 GLU cc_start: 0.9062 (tt0) cc_final: 0.8556 (tm-30) REVERT: F 470 MET cc_start: 0.7648 (tpt) cc_final: 0.7401 (tpt) REVERT: F 474 MET cc_start: 0.6909 (tpp) cc_final: 0.6390 (mmp) outliers start: 84 outliers final: 35 residues processed: 272 average time/residue: 0.1790 time to fit residues: 81.7911 Evaluate side-chains 226 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 480 PRO Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 86 optimal weight: 5.9990 chunk 359 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 294 optimal weight: 5.9990 overall best weight: 1.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1044 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.115564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.086448 restraints weight = 73865.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.084896 restraints weight = 67287.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085551 restraints weight = 71103.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.085769 restraints weight = 50377.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.086018 restraints weight = 43520.282| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30450 Z= 0.130 Angle : 0.573 8.136 41481 Z= 0.308 Chirality : 0.043 0.233 4725 Planarity : 0.004 0.045 5115 Dihedral : 15.068 138.631 4954 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.04 % Allowed : 13.94 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.21 (0.14), residues: 3539 helix: 1.12 (0.14), residues: 1435 sheet: -0.11 (0.26), residues: 368 loop : -1.25 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 363 TYR 0.019 0.001 TYR F 143 PHE 0.015 0.001 PHE C 828 TRP 0.015 0.001 TRP D 33 HIS 0.008 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (30448) covalent geometry : angle 0.57324 / 0.31 (41481) hydrogen bonds : bond 0.04417 / 4.97 ( 1331) hydrogen bonds : angle 4.42069 / 4.91 ( 3750) metal coordination : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 196 time to evaluate : 1.151 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: A 229 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: B 78 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8583 (tp) REVERT: B 107 ILE cc_start: 0.5928 (mm) cc_final: 0.5540 (tp) REVERT: B 188 GLU cc_start: 0.4308 (OUTLIER) cc_final: 0.4078 (pm20) REVERT: B 194 GLN cc_start: 0.1099 (OUTLIER) cc_final: 0.0213 (tt0) REVERT: C 185 ASP cc_start: 0.8408 (t70) cc_final: 0.7687 (t0) REVERT: C 194 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8037 (pp) REVERT: C 1066 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8260 (mtm) REVERT: C 1315 MET cc_start: 0.7436 (ptp) cc_final: 0.7159 (ptt) REVERT: D 165 TYR cc_start: 0.7472 (t80) cc_final: 0.6765 (t80) REVERT: D 869 CYS cc_start: 0.8660 (t) cc_final: 0.8253 (t) REVERT: D 1040 MET cc_start: 0.4582 (pmm) cc_final: 0.4312 (pmm) REVERT: D 1095 MET cc_start: 0.4537 (mmt) cc_final: 0.4127 (ptm) REVERT: D 1189 MET cc_start: 0.7286 (tmm) cc_final: 0.6952 (tmm) REVERT: D 1273 ASP cc_start: 0.6716 (t0) cc_final: 0.6401 (t0) REVERT: E 8 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7730 (p0) REVERT: E 55 GLU cc_start: 0.7339 (pp20) cc_final: 0.7087 (pp20) REVERT: E 71 GLU cc_start: 0.9090 (tt0) cc_final: 0.8515 (tm-30) REVERT: F 470 MET cc_start: 0.7570 (tpt) cc_final: 0.7316 (tpt) REVERT: F 474 MET cc_start: 0.6961 (tpp) cc_final: 0.6447 (mmp) outliers start: 63 outliers final: 37 residues processed: 241 average time/residue: 0.1755 time to fit residues: 71.6139 Evaluate side-chains 222 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 185 TYR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 480 PRO Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 330 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 258 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 293 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 chunk 334 optimal weight: 30.0000 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.115328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.086028 restraints weight = 74324.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.084469 restraints weight = 66276.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.085329 restraints weight = 67549.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.085445 restraints weight = 48223.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.085794 restraints weight = 42425.304| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30450 Z= 0.125 Angle : 0.568 9.605 41481 Z= 0.302 Chirality : 0.043 0.323 4725 Planarity : 0.004 0.045 5115 Dihedral : 14.948 137.777 4952 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.20 % Allowed : 14.93 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.05 (0.14), residues: 3539 helix: 1.24 (0.14), residues: 1437 sheet: 0.09 (0.27), residues: 352 loop : -1.18 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG F 150 TYR 0.017 0.001 TYR A 185 PHE 0.013 0.001 PHE C 828 TRP 0.015 0.001 TRP D1193 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (30448) covalent geometry : angle 0.56797 / 0.30 (41481) hydrogen bonds : bond 0.04184 / 4.71 ( 1331) hydrogen bonds : angle 4.32106 / 4.83 ( 3750) metal coordination : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 189 time to evaluate : 1.170 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6161 (pm20) REVERT: A 229 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6629 (tp30) REVERT: B 78 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8598 (tp) REVERT: B 188 GLU cc_start: 0.4207 (OUTLIER) cc_final: 0.3984 (pm20) REVERT: B 194 GLN cc_start: 0.1058 (OUTLIER) cc_final: 0.0192 (tt0) REVERT: C 185 ASP cc_start: 0.8024 (t70) cc_final: 0.7390 (t0) REVERT: C 194 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8075 (pp) REVERT: C 1066 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8203 (mtm) REVERT: D 479 GLU cc_start: 0.7388 (tt0) cc_final: 0.7073 (tt0) REVERT: D 740 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8514 (tt) REVERT: D 869 CYS cc_start: 0.8647 (t) cc_final: 0.8275 (t) REVERT: D 1040 MET cc_start: 0.4588 (pmm) cc_final: 0.4264 (pmm) REVERT: D 1095 MET cc_start: 0.4574 (mmt) cc_final: 0.4158 (ptm) REVERT: D 1189 MET cc_start: 0.7407 (tmm) cc_final: 0.7073 (tmm) REVERT: D 1273 ASP cc_start: 0.6742 (t0) cc_final: 0.6513 (t0) REVERT: E 55 GLU cc_start: 0.7268 (pp20) cc_final: 0.6635 (pp20) REVERT: E 71 GLU cc_start: 0.9143 (tt0) cc_final: 0.8612 (tm-30) REVERT: E 72 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8446 (tm-30) REVERT: E 73 GLN cc_start: 0.7290 (pp30) cc_final: 0.6840 (pp30) REVERT: F 273 MET cc_start: 0.7317 (mmm) cc_final: 0.6946 (mmt) REVERT: F 470 MET cc_start: 0.7620 (tpt) cc_final: 0.7360 (tpt) REVERT: F 474 MET cc_start: 0.6936 (tpp) cc_final: 0.6416 (mmp) outliers start: 68 outliers final: 48 residues processed: 238 average time/residue: 0.1767 time to fit residues: 70.8688 Evaluate side-chains 235 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 740 LEU Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 480 PRO Chi-restraints excluded: chain F residue 483 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 180 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 357 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 GLN C 832 HIS C1157 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 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 = 0.3786 r_free = 0.3786 target = 0.111871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.082714 restraints weight = 73998.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.081300 restraints weight = 69083.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.082030 restraints weight = 73193.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082293 restraints weight = 50493.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.082849 restraints weight = 44445.527| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 30450 Z= 0.195 Angle : 0.627 10.464 41481 Z= 0.332 Chirality : 0.044 0.370 4725 Planarity : 0.004 0.048 5115 Dihedral : 14.999 140.193 4952 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.89 % Allowed : 15.29 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.13 (0.14), residues: 3539 helix: 1.15 (0.14), residues: 1439 sheet: 0.11 (0.27), residues: 361 loop : -1.22 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG F 364 TYR 0.019 0.002 TYR F 148 PHE 0.015 0.002 PHE D 437 TRP 0.017 0.002 TRP D1193 HIS 0.013 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (30448) covalent geometry : angle 0.62660 / 0.33 (41481) hydrogen bonds : bond 0.04784 / 5.36 ( 1331) hydrogen bonds : angle 4.42299 / 4.96 ( 3750) metal coordination : bond 0.00371 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 183 time to evaluate : 1.269 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: A 185 TYR cc_start: 0.9119 (p90) cc_final: 0.8770 (p90) REVERT: B 23 HIS cc_start: 0.6961 (OUTLIER) cc_final: 0.6745 (t70) REVERT: B 86 LYS cc_start: 0.7472 (ttmt) cc_final: 0.7256 (ttmm) REVERT: B 207 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7140 (t) REVERT: C 185 ASP cc_start: 0.8191 (t70) cc_final: 0.7564 (t0) REVERT: C 341 LEU cc_start: 0.6732 (pt) cc_final: 0.6112 (mm) REVERT: C 1170 MET cc_start: 0.8258 (tpp) cc_final: 0.8032 (mmp) REVERT: C 1289 GLU cc_start: 0.7909 (pt0) cc_final: 0.7531 (pt0) REVERT: D 140 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7866 (m-10) REVERT: D 157 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: D 644 MET cc_start: 0.8789 (ptp) cc_final: 0.8314 (ptp) REVERT: D 869 CYS cc_start: 0.8645 (t) cc_final: 0.8257 (t) REVERT: D 979 ASN cc_start: 0.7166 (p0) cc_final: 0.6586 (p0) REVERT: D 1040 MET cc_start: 0.4646 (pmm) cc_final: 0.4266 (pmm) REVERT: D 1189 MET cc_start: 0.7547 (tmm) cc_final: 0.7231 (tmm) REVERT: E 55 GLU cc_start: 0.7196 (pp20) cc_final: 0.6555 (pp20) REVERT: E 70 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7923 (tm-30) REVERT: E 71 GLU cc_start: 0.9174 (tt0) cc_final: 0.8576 (tm-30) REVERT: E 72 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8380 (tm-30) REVERT: F 141 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7661 (mt) REVERT: F 286 LEU cc_start: 0.3887 (OUTLIER) cc_final: 0.3483 (pp) outliers start: 89 outliers final: 60 residues processed: 256 average time/residue: 0.1737 time to fit residues: 76.3343 Evaluate side-chains 241 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 480 PRO Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 199 optimal weight: 0.0770 chunk 138 optimal weight: 4.9990 chunk 349 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 334 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 291 optimal weight: 40.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 194 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.112602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083466 restraints weight = 73656.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081970 restraints weight = 67850.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.083034 restraints weight = 67030.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.083091 restraints weight = 47623.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083766 restraints weight = 42277.392| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30450 Z= 0.129 Angle : 0.574 11.611 41481 Z= 0.302 Chirality : 0.043 0.346 4725 Planarity : 0.004 0.047 5115 Dihedral : 14.882 138.994 4944 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.17 % Allowed : 16.84 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.03 (0.14), residues: 3539 helix: 1.31 (0.14), residues: 1440 sheet: 0.20 (0.27), residues: 359 loop : -1.15 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 976 TYR 0.018 0.001 TYR F 148 PHE 0.012 0.001 PHE C 405 TRP 0.051 0.002 TRP C 997 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (30448) covalent geometry : angle 0.57420 / 0.30 (41481) hydrogen bonds : bond 0.04194 / 4.73 ( 1331) hydrogen bonds : angle 4.27276 / 4.83 ( 3750) metal coordination : bond 0.00116 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 1.173 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6235 (pm20) REVERT: A 185 TYR cc_start: 0.9118 (p90) cc_final: 0.8780 (p90) REVERT: B 86 LYS cc_start: 0.7536 (ttmt) cc_final: 0.7234 (ttmm) REVERT: C 185 ASP cc_start: 0.8112 (t70) cc_final: 0.7503 (t0) REVERT: C 341 LEU cc_start: 0.6760 (pt) cc_final: 0.6213 (mm) REVERT: C 459 MET cc_start: 0.8354 (mtt) cc_final: 0.8026 (mtt) REVERT: C 635 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.8952 (p) REVERT: C 1170 MET cc_start: 0.8090 (tpp) cc_final: 0.7876 (mmp) REVERT: C 1289 GLU cc_start: 0.7859 (pt0) cc_final: 0.7545 (pt0) REVERT: C 1304 MET cc_start: 0.8904 (tpp) cc_final: 0.8667 (tpp) REVERT: D 140 TYR cc_start: 0.8238 (OUTLIER) cc_final: 0.8034 (m-10) REVERT: D 644 MET cc_start: 0.8778 (ptp) cc_final: 0.8318 (ptp) REVERT: D 869 CYS cc_start: 0.8630 (t) cc_final: 0.8229 (t) REVERT: D 1040 MET cc_start: 0.4615 (pmm) cc_final: 0.4214 (pmm) REVERT: D 1189 MET cc_start: 0.7734 (tmm) cc_final: 0.7407 (tmm) REVERT: E 55 GLU cc_start: 0.7193 (pp20) cc_final: 0.6474 (pp20) REVERT: E 71 GLU cc_start: 0.9140 (tt0) cc_final: 0.8568 (tm-30) REVERT: E 72 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8284 (tm-30) REVERT: E 73 GLN cc_start: 0.7310 (pp30) cc_final: 0.6881 (pp30) REVERT: F 141 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7365 (mt) REVERT: F 286 LEU cc_start: 0.4589 (OUTLIER) cc_final: 0.4155 (pp) REVERT: F 322 MET cc_start: 0.6768 (tpt) cc_final: 0.4589 (ptt) outliers start: 67 outliers final: 48 residues processed: 246 average time/residue: 0.1767 time to fit residues: 73.6234 Evaluate side-chains 234 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 140 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 480 PRO Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 168 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1044 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.112823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084099 restraints weight = 73812.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.082356 restraints weight = 72752.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083479 restraints weight = 63897.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083807 restraints weight = 45053.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.084171 restraints weight = 42475.950| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 30450 Z= 0.116 Angle : 0.563 13.023 41481 Z= 0.295 Chirality : 0.042 0.382 4725 Planarity : 0.004 0.045 5115 Dihedral : 14.856 138.095 4942 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.10 % Allowed : 17.23 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.13 (0.14), residues: 3539 helix: 1.40 (0.14), residues: 1435 sheet: 0.20 (0.27), residues: 345 loop : -1.08 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 363 TYR 0.022 0.001 TYR C 291 PHE 0.013 0.001 PHE C1323 TRP 0.048 0.002 TRP C 997 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (30448) covalent geometry : angle 0.56279 / 0.30 (41481) hydrogen bonds : bond 0.03938 / 4.42 ( 1331) hydrogen bonds : angle 4.17926 / 4.72 ( 3750) metal coordination : bond 0.00126 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 1.253 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6248 (pm20) REVERT: A 145 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8488 (ttmm) REVERT: A 185 TYR cc_start: 0.9033 (p90) cc_final: 0.8695 (p90) REVERT: B 62 ASP cc_start: 0.5692 (p0) cc_final: 0.5340 (m-30) REVERT: B 86 LYS cc_start: 0.7551 (ttmt) cc_final: 0.7260 (ttmm) REVERT: C 124 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8533 (ptm) REVERT: C 185 ASP cc_start: 0.8001 (t70) cc_final: 0.7448 (t0) REVERT: C 341 LEU cc_start: 0.6782 (pt) cc_final: 0.6247 (mm) REVERT: C 635 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8938 (p) REVERT: C 1170 MET cc_start: 0.8100 (tpp) cc_final: 0.7897 (mmp) REVERT: D 466 MET cc_start: 0.7395 (ptp) cc_final: 0.7014 (ptp) REVERT: D 644 MET cc_start: 0.8813 (ptp) cc_final: 0.8460 (ptp) REVERT: D 743 MET cc_start: 0.8303 (tpp) cc_final: 0.7957 (tpt) REVERT: D 869 CYS cc_start: 0.8561 (t) cc_final: 0.8182 (t) REVERT: D 1189 MET cc_start: 0.7566 (tmm) cc_final: 0.7317 (tmm) REVERT: E 55 GLU cc_start: 0.7154 (pp20) cc_final: 0.6413 (pp20) REVERT: E 71 GLU cc_start: 0.9129 (tt0) cc_final: 0.8592 (tm-30) REVERT: E 72 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8277 (tm-30) REVERT: E 73 GLN cc_start: 0.7377 (pp30) cc_final: 0.6915 (pp30) REVERT: F 141 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7316 (mt) REVERT: F 273 MET cc_start: 0.7273 (mmm) cc_final: 0.6799 (mmt) REVERT: F 286 LEU cc_start: 0.3376 (OUTLIER) cc_final: 0.2989 (pp) REVERT: F 322 MET cc_start: 0.6549 (tpt) cc_final: 0.4136 (ptt) REVERT: F 489 MET cc_start: 0.4853 (ptp) cc_final: 0.2738 (ttt) outliers start: 65 outliers final: 49 residues processed: 237 average time/residue: 0.1764 time to fit residues: 70.9659 Evaluate side-chains 233 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 480 PRO Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 497 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 74 optimal weight: 7.9990 chunk 114 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 290 optimal weight: 40.0000 chunk 240 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 230 optimal weight: 0.5980 chunk 271 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 153 ASN D 708 ASN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.111862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.083143 restraints weight = 73594.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081337 restraints weight = 70459.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082410 restraints weight = 68165.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082465 restraints weight = 49505.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083316 restraints weight = 43205.724| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30450 Z= 0.137 Angle : 0.580 13.538 41481 Z= 0.303 Chirality : 0.042 0.374 4725 Planarity : 0.004 0.044 5115 Dihedral : 14.898 137.968 4940 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.10 % Allowed : 17.49 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.14 (0.14), residues: 3539 helix: 1.43 (0.14), residues: 1433 sheet: 0.17 (0.28), residues: 349 loop : -1.08 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 245 TYR 0.028 0.001 TYR C 291 PHE 0.014 0.001 PHE C 35 TRP 0.026 0.002 TRP C 997 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (30448) covalent geometry : angle 0.58001 / 0.30 (41481) hydrogen bonds : bond 0.04064 / 4.57 ( 1331) hydrogen bonds : angle 4.19654 / 4.78 ( 3750) metal coordination : bond 0.00219 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 1.218 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: A 145 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8410 (ttmm) REVERT: A 185 TYR cc_start: 0.9022 (p90) cc_final: 0.8674 (p90) REVERT: B 62 ASP cc_start: 0.5840 (p0) cc_final: 0.5556 (m-30) REVERT: B 86 LYS cc_start: 0.7627 (ttmt) cc_final: 0.7357 (ttmm) REVERT: C 124 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8540 (ptm) REVERT: C 185 ASP cc_start: 0.8025 (t70) cc_final: 0.7486 (t0) REVERT: C 341 LEU cc_start: 0.6871 (pt) cc_final: 0.6375 (mm) REVERT: C 635 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.8949 (p) REVERT: C 1170 MET cc_start: 0.8104 (tpp) cc_final: 0.7896 (mmp) REVERT: D 743 MET cc_start: 0.8655 (tpp) cc_final: 0.8330 (tpt) REVERT: D 869 CYS cc_start: 0.8587 (t) cc_final: 0.8214 (t) REVERT: D 979 ASN cc_start: 0.7655 (p0) cc_final: 0.7086 (p0) REVERT: D 1189 MET cc_start: 0.7577 (tmm) cc_final: 0.7345 (tmm) REVERT: E 55 GLU cc_start: 0.7094 (pp20) cc_final: 0.6400 (pp20) REVERT: E 71 GLU cc_start: 0.9149 (tt0) cc_final: 0.8628 (tm-30) REVERT: E 72 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8281 (tm-30) REVERT: E 73 GLN cc_start: 0.7273 (pp30) cc_final: 0.6854 (pp30) REVERT: F 141 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7716 (mt) REVERT: F 286 LEU cc_start: 0.3419 (OUTLIER) cc_final: 0.3018 (pp) REVERT: F 322 MET cc_start: 0.6508 (tpt) cc_final: 0.4122 (ptt) REVERT: F 489 MET cc_start: 0.4071 (ptp) cc_final: 0.2533 (ttt) outliers start: 65 outliers final: 53 residues processed: 230 average time/residue: 0.1773 time to fit residues: 69.4348 Evaluate side-chains 236 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 177 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 480 PRO Chi-restraints excluded: chain F residue 483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 298 optimal weight: 30.0000 chunk 256 optimal weight: 5.9990 chunk 350 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 322 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 210 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 349 optimal weight: 0.8980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.111346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082844 restraints weight = 73362.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081857 restraints weight = 68967.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.082226 restraints weight = 76199.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082726 restraints weight = 50230.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.083218 restraints weight = 43082.230| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30450 Z= 0.136 Angle : 0.592 17.518 41481 Z= 0.308 Chirality : 0.043 0.383 4725 Planarity : 0.004 0.044 5115 Dihedral : 14.948 138.163 4940 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.10 % Allowed : 17.40 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.13 (0.14), residues: 3539 helix: 1.36 (0.14), residues: 1440 sheet: 0.23 (0.28), residues: 347 loop : -1.06 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 976 TYR 0.031 0.001 TYR C 291 PHE 0.013 0.001 PHE C 35 TRP 0.034 0.002 TRP C 997 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (30448) covalent geometry : angle 0.59189 / 0.31 (41481) hydrogen bonds : bond 0.04080 / 4.59 ( 1331) hydrogen bonds : angle 4.18092 / 4.75 ( 3750) metal coordination : bond 0.00202 / 0.10 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7078 Ramachandran restraints generated. 3539 Oldfield, 0 Emsley, 3539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: A 145 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8439 (ttmm) REVERT: A 185 TYR cc_start: 0.9016 (p90) cc_final: 0.8791 (p90) REVERT: B 62 ASP cc_start: 0.5907 (p0) cc_final: 0.5581 (m-30) REVERT: C 185 ASP cc_start: 0.8034 (t70) cc_final: 0.7519 (t0) REVERT: C 341 LEU cc_start: 0.6994 (pt) cc_final: 0.6421 (mm) REVERT: C 635 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.8956 (p) REVERT: D 466 MET cc_start: 0.7466 (ptp) cc_final: 0.7114 (ptp) REVERT: D 743 MET cc_start: 0.8562 (tpp) cc_final: 0.8280 (tpt) REVERT: D 869 CYS cc_start: 0.8621 (t) cc_final: 0.8241 (t) REVERT: D 1189 MET cc_start: 0.7455 (tmm) cc_final: 0.7253 (tmm) REVERT: E 55 GLU cc_start: 0.7110 (pp20) cc_final: 0.6412 (pp20) REVERT: E 71 GLU cc_start: 0.9171 (tt0) cc_final: 0.8629 (tm-30) REVERT: E 73 GLN cc_start: 0.7349 (pp30) cc_final: 0.7037 (pp30) REVERT: F 141 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7741 (mt) REVERT: F 273 MET cc_start: 0.7423 (mmm) cc_final: 0.6824 (mmt) REVERT: F 286 LEU cc_start: 0.4091 (OUTLIER) cc_final: 0.3640 (pp) REVERT: F 322 MET cc_start: 0.6483 (tpt) cc_final: 0.4112 (ptt) REVERT: F 489 MET cc_start: 0.3974 (ptp) cc_final: 0.2540 (ttt) outliers start: 65 outliers final: 54 residues processed: 232 average time/residue: 0.1824 time to fit residues: 71.5781 Evaluate side-chains 234 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 175 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 480 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 353 optimal weight: 10.0000 chunk 310 optimal weight: 3.9990 chunk 270 optimal weight: 9.9990 chunk 246 optimal weight: 0.6980 chunk 254 optimal weight: 8.9990 chunk 41 optimal weight: 30.0000 chunk 21 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 218 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN C1008 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.109998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.081083 restraints weight = 73913.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079957 restraints weight = 67118.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080419 restraints weight = 72746.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.080653 restraints weight = 50392.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081094 restraints weight = 43572.509| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30450 Z= 0.165 Angle : 0.603 13.214 41481 Z= 0.314 Chirality : 0.043 0.398 4725 Planarity : 0.004 0.044 5115 Dihedral : 15.024 138.913 4940 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.17 % Allowed : 17.63 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.11 (0.14), residues: 3539 helix: 1.36 (0.14), residues: 1440 sheet: 0.21 (0.28), residues: 361 loop : -1.09 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 976 TYR 0.030 0.001 TYR C 291 PHE 0.017 0.001 PHE C 35 TRP 0.058 0.003 TRP F 315 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (30448) covalent geometry : angle 0.60297 / 0.31 (41481) hydrogen bonds : bond 0.04358 / 4.92 ( 1331) hydrogen bonds : angle 4.25147 / 4.84 ( 3750) metal coordination : bond 0.00393 / 0.20 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4234.29 seconds wall clock time: 74 minutes 23.78 seconds (4463.78 seconds total)