Starting phenix.real_space_refine on Wed Oct 28 22:03:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4e_24148/10_2026/7n4e_24148_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4e_24148/10_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_24148/10_2026/7n4e_24148_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4e_24148/10_2026/7n4e_24148_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n4e_24148/10_2026/7n4e_24148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4e_24148/10_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: 5.32, per 1000 atoms: 0.18 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: 2.25 Conformation dependent library (CDL) restraints added in 1.2 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: 3.92 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: 7.66 Time building geometry restraints manager: 2.94 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 1.20e-02 6.94e+03 7.78e+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 119.70 134.23 -14.53 1.20e+00 6.94e-01 1.47e+02 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: 4275 0.078 - 0.157: 435 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 32.650 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- 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= 0.257 Angle : 0.729 14.761 41481 Z= 0.448 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 / 0.26 (30448) covalent geometry : angle 0.72938 / 0.45 (41481) hydrogen bonds : bond 0.14402 / 16.20 ( 1331) hydrogen bonds : angle 6.02335 / 6.61 ( 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 : 1.002 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: 0.1736 (tt0) REVERT: B 224 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7744 (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: 0.7836 (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: 0.6684 (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) REVERT: F 483 LEU cc_start: 0.8104 (mt) cc_final: 0.7904 (mt) outliers start: 106 outliers final: 17 residues processed: 337 average time/residue: 0.1921 time to fit residues: 104.4043 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 : 0.798 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.124419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095354 restraints weight = 75466.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.093862 restraints weight = 63385.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094918 restraints weight = 59998.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094888 restraints weight = 42558.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.095272 restraints weight = 38574.426| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30450 Z= 0.135 Angle : 0.597 10.951 41481 Z= 0.319 Chirality : 0.044 0.211 4725 Planarity : 0.004 0.048 5115 Dihedral : 15.696 151.456 4997 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.71 % Allowed : 8.25 % 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: -0.35 (0.14), residues: 3539 helix: 0.98 (0.14), residues: 1433 sheet: -0.15 (0.27), residues: 362 loop : -1.31 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 182 TYR 0.030 0.001 TYR D 165 PHE 0.017 0.001 PHE B 231 TRP 0.022 0.001 TRP D 33 HIS 0.005 0.001 HIS D 865 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (30448) covalent geometry : angle 0.59656 / 0.32 (41481) hydrogen bonds : bond 0.04810 / 5.40 ( 1331) hydrogen bonds : angle 4.79503 / 5.30 ( 3750) metal coordination : bond 0.00129 / 0.06 ( 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 285 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 1.007 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 159 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 229 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5758 (tm-30) REVERT: B 71 LYS cc_start: 0.6859 (tptp) cc_final: 0.6521 (tptp) REVERT: B 78 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8354 (tp) REVERT: B 107 ILE cc_start: 0.6010 (mm) cc_final: 0.5606 (tp) REVERT: B 194 GLN cc_start: 0.0787 (OUTLIER) cc_final: 0.0005 (tt0) REVERT: B 224 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7999 (mt) REVERT: C 185 ASP cc_start: 0.8076 (t70) cc_final: 0.7495 (t0) REVERT: C 237 LEU cc_start: 0.6821 (mt) cc_final: 0.6581 (mt) REVERT: C 951 MET cc_start: 0.8206 (mmm) cc_final: 0.7865 (mmm) REVERT: C 1290 MET cc_start: 0.8213 (mtt) cc_final: 0.8007 (mtt) REVERT: D 140 TYR cc_start: 0.8038 (m-10) cc_final: 0.7539 (m-10) REVERT: D 525 MET cc_start: 0.6066 (tpp) cc_final: 0.5638 (mmm) REVERT: D 527 LEU cc_start: 0.8279 (mt) cc_final: 0.7898 (mt) REVERT: D 869 CYS cc_start: 0.8589 (t) cc_final: 0.8148 (t) REVERT: D 1095 MET cc_start: 0.4405 (mmt) cc_final: 0.4051 (ptm) REVERT: E 41 GLU cc_start: 0.7609 (pp20) cc_final: 0.7367 (pp20) REVERT: E 67 ARG cc_start: 0.8308 (ttp80) cc_final: 0.8011 (tpp-160) REVERT: E 69 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8184 (tpp80) REVERT: E 70 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7779 (tm-30) REVERT: E 71 GLU cc_start: 0.8993 (tt0) cc_final: 0.8475 (tm-30) REVERT: F 487 MET cc_start: 0.6489 (ttt) cc_final: 0.6281 (ttm) outliers start: 53 outliers final: 33 residues processed: 265 average time/residue: 0.1818 time to fit residues: 80.1384 Evaluate side-chains 237 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 172 LEU Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 38 THR 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 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 130 MET 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 480 PRO Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [213, 95, 31, 211, 166, 85, 218, 21, 241, 62, 44] chunk 213 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 218 optimal weight: 0.3980 chunk 21 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 23 HIS B 147 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 811 ASN C1257 GLN ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1114 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.118357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.089511 restraints weight = 75029.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087938 restraints weight = 68889.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.089055 restraints weight = 68635.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089083 restraints weight = 47315.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.090036 restraints weight = 42279.225| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30450 Z= 0.176 Angle : 0.634 9.135 41481 Z= 0.337 Chirality : 0.045 0.195 4725 Planarity : 0.004 0.047 5115 Dihedral : 15.189 134.649 4963 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.50 % Allowed : 11.15 % Favored : 86.35 % 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: -0.26 (0.14), residues: 3539 helix: 1.08 (0.14), residues: 1434 sheet: -0.11 (0.27), residues: 360 loop : -1.28 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 191 TYR 0.026 0.002 TYR D 165 PHE 0.016 0.002 PHE D 437 TRP 0.026 0.002 TRP D 33 HIS 0.006 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (30448) covalent geometry : angle 0.63394 / 0.34 (41481) hydrogen bonds : bond 0.04757 / 5.40 ( 1331) hydrogen bonds : angle 4.53164 / 5.02 ( 3750) metal coordination : bond 0.00096 / 0.05 ( 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 290 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 213 time to evaluate : 1.125 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.6054 (pm20) REVERT: A 27 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8115 (p) REVERT: A 159 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7840 (mm) REVERT: A 185 TYR cc_start: 0.8292 (p90) cc_final: 0.7940 (p90) REVERT: A 229 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6284 (tp30) REVERT: A 232 VAL cc_start: 0.5807 (OUTLIER) cc_final: 0.5483 (p) REVERT: B 78 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8457 (tp) REVERT: B 107 ILE cc_start: 0.5903 (mm) cc_final: 0.5521 (tp) REVERT: B 132 HIS cc_start: 0.7445 (m-70) cc_final: 0.7091 (m-70) REVERT: B 188 GLU cc_start: 0.4068 (OUTLIER) cc_final: 0.3683 (pm20) REVERT: B 194 GLN cc_start: 0.0765 (OUTLIER) cc_final: -0.0008 (tt0) REVERT: C 185 ASP cc_start: 0.8328 (t70) cc_final: 0.7704 (t0) REVERT: C 194 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7630 (pp) REVERT: C 315 MET cc_start: 0.5672 (ppp) cc_final: 0.5165 (ppp) REVERT: C 951 MET cc_start: 0.8449 (mmm) cc_final: 0.8130 (mmm) REVERT: C 1010 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6869 (tp40) REVERT: D 165 TYR cc_start: 0.7067 (t80) cc_final: 0.6426 (t80) REVERT: D 527 LEU cc_start: 0.8801 (mt) cc_final: 0.8526 (mt) REVERT: D 869 CYS cc_start: 0.8581 (t) cc_final: 0.8177 (t) REVERT: D 1040 MET cc_start: 0.5357 (pmm) cc_final: 0.5040 (pmm) REVERT: D 1095 MET cc_start: 0.4439 (mmt) cc_final: 0.4070 (ptm) REVERT: E 15 ASN cc_start: 0.6729 (t0) cc_final: 0.6314 (t0) REVERT: E 43 ASN cc_start: 0.8446 (t0) cc_final: 0.8177 (t0) REVERT: E 71 GLU cc_start: 0.9017 (tt0) cc_final: 0.8547 (tm-30) outliers start: 77 outliers final: 37 residues processed: 267 average time/residue: 0.1722 time to fit residues: 77.4972 Evaluate side-chains 231 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 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 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 A residue 232 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 70 THR Chi-restraints excluded: chain B residue 78 ILE 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 164 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 311 CYS 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 811 ASN 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 C residue 1281 TYR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 145 VAL 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: [86, 359, 98, 113, 212, 196, 279, 161, 187, 139, 294] chunk 86 optimal weight: 8.9990 chunk 359 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 279 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 187 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 294 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 GLN D 450 HIS D1044 GLN ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.117864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088924 restraints weight = 74048.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087801 restraints weight = 66172.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088587 restraints weight = 67518.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088897 restraints weight = 45119.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.089418 restraints weight = 40409.258| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30450 Z= 0.128 Angle : 0.559 8.328 41481 Z= 0.298 Chirality : 0.043 0.225 4725 Planarity : 0.004 0.047 5115 Dihedral : 15.001 137.218 4953 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.10 % Allowed : 13.09 % Favored : 84.81 % 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: -0.09 (0.14), residues: 3539 helix: 1.23 (0.14), residues: 1436 sheet: 0.02 (0.27), residues: 357 loop : -1.20 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 363 TYR 0.022 0.001 TYR F 143 PHE 0.012 0.001 PHE C 405 TRP 0.015 0.001 TRP D1193 HIS 0.005 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (30448) covalent geometry : angle 0.55864 / 0.30 (41481) hydrogen bonds : bond 0.04166 / 4.71 ( 1331) hydrogen bonds : angle 4.35896 / 4.85 ( 3750) metal coordination : bond 0.00064 / 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 265 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 0.858 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.6047 (pm20) REVERT: A 41 ASN cc_start: 0.8226 (OUTLIER) cc_final: 0.7982 (t0) REVERT: A 229 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6348 (tp30) REVERT: B 35 PHE cc_start: 0.5421 (m-80) cc_final: 0.5202 (m-80) REVERT: B 78 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8375 (tp) REVERT: B 107 ILE cc_start: 0.5705 (mm) cc_final: 0.5337 (tp) REVERT: B 194 GLN cc_start: 0.1102 (OUTLIER) cc_final: 0.0243 (tt0) REVERT: C 185 ASP cc_start: 0.8324 (t70) cc_final: 0.7647 (t0) REVERT: C 194 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7815 (pp) REVERT: C 315 MET cc_start: 0.5691 (ppp) cc_final: 0.5213 (ppp) REVERT: C 870 ILE cc_start: 0.9000 (mp) cc_final: 0.8734 (mt) REVERT: C 951 MET cc_start: 0.8218 (mmm) cc_final: 0.7925 (mmm) REVERT: C 1010 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6987 (tp40) REVERT: D 165 TYR cc_start: 0.7128 (t80) cc_final: 0.6549 (t80) REVERT: D 479 GLU cc_start: 0.8091 (tt0) cc_final: 0.7760 (tt0) REVERT: D 725 MET cc_start: 0.9071 (mtt) cc_final: 0.8785 (mtm) REVERT: D 869 CYS cc_start: 0.8568 (t) cc_final: 0.8157 (t) REVERT: D 1040 MET cc_start: 0.4407 (pmm) cc_final: 0.4108 (pmm) REVERT: D 1095 MET cc_start: 0.4418 (mmt) cc_final: 0.4081 (ptm) REVERT: D 1273 ASP cc_start: 0.6686 (t0) cc_final: 0.6438 (t0) REVERT: D 1369 ARG cc_start: 0.7468 (ttt180) cc_final: 0.7242 (ttp80) REVERT: E 8 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7452 (p0) REVERT: E 55 GLU cc_start: 0.7379 (pp20) cc_final: 0.6648 (pp20) REVERT: E 71 GLU cc_start: 0.9068 (tt0) cc_final: 0.8483 (tm-30) REVERT: F 101 TYR cc_start: 0.9372 (t80) cc_final: 0.9099 (t80) REVERT: F 474 MET cc_start: 0.7397 (tpp) cc_final: 0.6450 (mmp) outliers start: 65 outliers final: 32 residues processed: 248 average time/residue: 0.1691 time to fit residues: 70.9826 Evaluate side-chains 227 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 41 ASN 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 229 GLU 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 68 TYR Chi-restraints excluded: chain B residue 78 ILE 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 223 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 805 MET Chi-restraints excluded: chain C residue 811 ASN 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 D residue 552 ILE 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 8 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain F residue 480 PRO Chi-restraints excluded: chain F residue 483 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [330, 244, 182, 99, 258, 74, 293, 179, 51, 187, 334] chunk 330 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 258 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 293 optimal weight: 30.0000 chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 334 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 120 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.116144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.087084 restraints weight = 74561.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.086233 restraints weight = 68535.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087002 restraints weight = 66359.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086935 restraints weight = 46916.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.087242 restraints weight = 41437.477| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30450 Z= 0.145 Angle : 0.564 9.478 41481 Z= 0.300 Chirality : 0.042 0.194 4725 Planarity : 0.004 0.048 5115 Dihedral : 14.923 136.607 4952 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.10 % Allowed : 14.44 % Favored : 83.46 % 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: 1.27 (0.14), residues: 1436 sheet: 0.04 (0.26), residues: 365 loop : -1.15 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.000 ARG F 150 TYR 0.017 0.001 TYR A 185 PHE 0.010 0.001 PHE D 437 TRP 0.013 0.001 TRP D1193 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (30448) covalent geometry : angle 0.56362 / 0.30 (41481) hydrogen bonds : bond 0.04219 / 4.78 ( 1331) hydrogen bonds : angle 4.33208 / 4.83 ( 3750) metal coordination : bond 0.00103 / 0.05 ( 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: 65 poor density : 192 time to evaluate : 1.070 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.6108 (pm20) REVERT: A 229 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6451 (tp30) REVERT: A 232 VAL cc_start: 0.6304 (OUTLIER) cc_final: 0.6018 (p) REVERT: B 107 ILE cc_start: 0.5792 (mm) cc_final: 0.5363 (tp) REVERT: B 194 GLN cc_start: 0.1106 (OUTLIER) cc_final: 0.0210 (tt0) REVERT: B 223 ILE cc_start: 0.7560 (mm) cc_final: 0.7274 (mm) REVERT: C 185 ASP cc_start: 0.8378 (t70) cc_final: 0.7707 (t0) REVERT: C 194 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7900 (pp) REVERT: C 315 MET cc_start: 0.5481 (ppp) cc_final: 0.5233 (ppp) REVERT: C 951 MET cc_start: 0.8258 (mmm) cc_final: 0.7978 (mmm) REVERT: D 165 TYR cc_start: 0.7382 (t80) cc_final: 0.6761 (t80) REVERT: D 479 GLU cc_start: 0.8128 (tt0) cc_final: 0.7832 (tt0) REVERT: D 525 MET cc_start: 0.6777 (mmm) cc_final: 0.6374 (ttt) REVERT: D 869 CYS cc_start: 0.8612 (t) cc_final: 0.8292 (t) REVERT: D 1040 MET cc_start: 0.4616 (pmm) cc_final: 0.4299 (pmm) REVERT: D 1095 MET cc_start: 0.4518 (mmt) cc_final: 0.4125 (ptm) REVERT: D 1273 ASP cc_start: 0.6749 (t0) cc_final: 0.6428 (t0) REVERT: D 1369 ARG cc_start: 0.7694 (ttt180) cc_final: 0.7285 (ttp80) REVERT: E 55 GLU cc_start: 0.7304 (pp20) cc_final: 0.6626 (pp20) REVERT: E 71 GLU cc_start: 0.9063 (tt0) cc_final: 0.8623 (tm-30) REVERT: E 73 GLN cc_start: 0.7206 (pp30) cc_final: 0.6665 (pp30) REVERT: F 150 ARG cc_start: 0.7646 (mmp80) cc_final: 0.7442 (mmt-90) REVERT: F 474 MET cc_start: 0.7395 (tpp) cc_final: 0.6461 (mmp) outliers start: 65 outliers final: 40 residues processed: 239 average time/residue: 0.1654 time to fit residues: 67.3698 Evaluate side-chains 223 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 229 GLU Chi-restraints excluded: chain A residue 232 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 187 VAL 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 164 THR Chi-restraints excluded: chain C residue 194 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 727 VAL Chi-restraints excluded: chain C residue 805 MET 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 C residue 1339 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 513 MET Chi-restraints excluded: chain D residue 552 ILE 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 1209 VAL Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 21 LEU 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: [180, 15, 242, 26, 357, 36, 297, 44, 226, 187, 8] chunk 180 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 242 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 297 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 187 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN C 343 HIS C 832 HIS C1157 GLN D 435 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.112271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083068 restraints weight = 73885.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081906 restraints weight = 67352.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.082309 restraints weight = 75455.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082780 restraints weight = 49617.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.083580 restraints weight = 43014.541| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30450 Z= 0.197 Angle : 0.642 10.570 41481 Z= 0.339 Chirality : 0.044 0.274 4725 Planarity : 0.004 0.047 5115 Dihedral : 14.960 139.222 4950 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.66 % Allowed : 14.76 % Favored : 82.57 % 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: 1.14 (0.14), residues: 1434 sheet: 0.01 (0.26), residues: 366 loop : -1.19 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 364 TYR 0.021 0.002 TYR F 148 PHE 0.017 0.002 PHE D 437 TRP 0.019 0.002 TRP D1193 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (30448) covalent geometry : angle 0.64170 / 0.34 (41481) hydrogen bonds : bond 0.04822 / 5.46 ( 1331) hydrogen bonds : angle 4.45627 / 5.00 ( 3750) metal coordination : bond 0.00304 / 0.15 ( 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 269 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 187 time to evaluate : 1.098 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: A 93 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 185 TYR cc_start: 0.9095 (p90) cc_final: 0.8766 (p90) REVERT: A 229 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6620 (tp30) REVERT: B 62 ASP cc_start: 0.5591 (p0) cc_final: 0.5021 (t0) REVERT: B 78 ILE cc_start: 0.9235 (tp) cc_final: 0.8945 (pt) REVERT: B 86 LYS cc_start: 0.7228 (ttmt) cc_final: 0.6984 (ttmm) REVERT: B 223 ILE cc_start: 0.8178 (mm) cc_final: 0.7937 (mm) REVERT: C 185 ASP cc_start: 0.8176 (t70) cc_final: 0.7586 (t0) REVERT: C 194 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (pp) REVERT: C 1289 GLU cc_start: 0.7846 (pt0) cc_final: 0.7587 (pt0) REVERT: D 140 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: D 479 GLU cc_start: 0.8008 (tt0) cc_final: 0.7794 (tt0) REVERT: D 869 CYS cc_start: 0.8653 (t) cc_final: 0.8247 (t) REVERT: D 979 ASN cc_start: 0.7163 (p0) cc_final: 0.6577 (p0) REVERT: D 1040 MET cc_start: 0.4598 (pmm) cc_final: 0.4223 (pmm) REVERT: E 55 GLU cc_start: 0.7204 (pp20) cc_final: 0.6557 (pp20) REVERT: E 69 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8273 (mmp80) REVERT: E 71 GLU cc_start: 0.9152 (tt0) cc_final: 0.8590 (tm-30) REVERT: F 141 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7737 (mt) REVERT: F 286 LEU cc_start: 0.4029 (OUTLIER) cc_final: 0.3699 (pp) outliers start: 82 outliers final: 58 residues processed: 251 average time/residue: 0.1697 time to fit residues: 72.7094 Evaluate side-chains 240 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 176 time to evaluate : 1.206 ------------------------------------------------------------------------------- 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 183 ILE 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 48 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 70 THR 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 135 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 217 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 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 1066 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1241 ASP 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 140 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 400 MET 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: [199, 138, 349, 162, 36, 171, 334, 297, 77, 291, 103] chunk 199 optimal weight: 0.0770 chunk 138 optimal weight: 0.9990 chunk 349 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 chunk 334 optimal weight: 3.9990 chunk 297 optimal weight: 8.9990 chunk 77 optimal weight: 0.0010 chunk 291 optimal weight: 50.0000 chunk 103 optimal weight: 0.9980 overall best weight: 0.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 194 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 = 0.3822 r_free = 0.3822 target = 0.114080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085056 restraints weight = 73435.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.083872 restraints weight = 66004.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.084853 restraints weight = 64100.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.084824 restraints weight = 43492.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.085373 restraints weight = 39621.494| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30450 Z= 0.110 Angle : 0.559 9.551 41481 Z= 0.294 Chirality : 0.042 0.284 4725 Planarity : 0.004 0.045 5115 Dihedral : 14.850 137.398 4947 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.94 % Allowed : 16.38 % Favored : 81.68 % 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: 0.10 (0.14), residues: 3539 helix: 1.35 (0.14), residues: 1440 sheet: 0.20 (0.27), residues: 351 loop : -1.08 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 976 TYR 0.021 0.001 TYR C 291 PHE 0.012 0.001 PHE C 405 TRP 0.046 0.002 TRP C 997 HIS 0.004 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (30448) covalent geometry : angle 0.55927 / 0.29 (41481) hydrogen bonds : bond 0.03972 / 4.51 ( 1331) hydrogen bonds : angle 4.22950 / 4.78 ( 3750) metal coordination : bond 0.00057 / 0.03 ( 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 248 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 188 time to evaluate : 1.126 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6231 (pm20) REVERT: A 93 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 159 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7089 (tp) REVERT: A 185 TYR cc_start: 0.9042 (p90) cc_final: 0.8544 (p90) REVERT: A 229 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6604 (tp30) REVERT: C 185 ASP cc_start: 0.8066 (t70) cc_final: 0.7487 (t0) REVERT: C 635 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8916 (p) REVERT: C 826 ASP cc_start: 0.7652 (p0) cc_final: 0.7398 (p0) REVERT: C 1289 GLU cc_start: 0.7769 (pt0) cc_final: 0.7475 (pt0) REVERT: C 1304 MET cc_start: 0.8705 (tpp) cc_final: 0.8427 (tpp) REVERT: D 194 LEU cc_start: 0.7436 (mt) cc_final: 0.7222 (mt) REVERT: D 644 MET cc_start: 0.8699 (ptp) cc_final: 0.8269 (ptp) REVERT: D 869 CYS cc_start: 0.8590 (t) cc_final: 0.8191 (t) REVERT: D 1040 MET cc_start: 0.4610 (pmm) cc_final: 0.4205 (pmm) REVERT: E 55 GLU cc_start: 0.7217 (pp20) cc_final: 0.6490 (pp20) REVERT: E 71 GLU cc_start: 0.9050 (tt0) cc_final: 0.8639 (tm-30) REVERT: F 273 MET cc_start: 0.7523 (mmm) cc_final: 0.7058 (mmt) REVERT: F 322 MET cc_start: 0.6516 (tpt) cc_final: 0.4093 (ptt) REVERT: F 474 MET cc_start: 0.6998 (tpp) cc_final: 0.6486 (mmp) outliers start: 60 outliers final: 40 residues processed: 231 average time/residue: 0.1699 time to fit residues: 66.5897 Evaluate side-chains 221 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 41 ASN 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 229 GLU 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 68 TYR 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 242 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 492 MET 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 1339 LEU Chi-restraints excluded: chain D residue 88 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 651 HIS 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 480 PRO Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [168, 263, 242, 157, 182, 239, 113, 61, 103, 119, 39] chunk 168 optimal weight: 0.7980 chunk 263 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 239 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 0.2980 chunk 119 optimal weight: 0.9990 chunk 39 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN D 716 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.114038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.085474 restraints weight = 73508.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.084008 restraints weight = 68580.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085124 restraints weight = 65953.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.085117 restraints weight = 45616.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085766 restraints weight = 40511.491| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 30450 Z= 0.111 Angle : 0.557 11.947 41481 Z= 0.291 Chirality : 0.042 0.254 4725 Planarity : 0.004 0.044 5115 Dihedral : 14.829 136.673 4945 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.97 % Allowed : 16.84 % Favored : 81.19 % 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: 0.15 (0.14), residues: 3539 helix: 1.38 (0.14), residues: 1442 sheet: 0.26 (0.27), residues: 340 loop : -1.04 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 944 TYR 0.026 0.001 TYR C 291 PHE 0.015 0.001 PHE C1323 TRP 0.042 0.002 TRP C 997 HIS 0.003 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (30448) covalent geometry : angle 0.55721 / 0.29 (41481) hydrogen bonds : bond 0.03871 / 4.39 ( 1331) hydrogen bonds : angle 4.16309 / 4.72 ( 3750) metal coordination : bond 0.00066 / 0.03 ( 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 247 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 186 time to evaluate : 0.936 Fit side-chains Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6250 (pm20) REVERT: A 185 TYR cc_start: 0.9023 (p90) cc_final: 0.8609 (p90) REVERT: B 62 ASP cc_start: 0.5445 (p0) cc_final: 0.5025 (m-30) REVERT: C 185 ASP cc_start: 0.8062 (t70) cc_final: 0.7495 (t0) REVERT: C 242 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7580 (p) REVERT: C 341 LEU cc_start: 0.6535 (pt) cc_final: 0.6137 (mm) REVERT: C 635 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8918 (p) REVERT: C 826 ASP cc_start: 0.7728 (p0) cc_final: 0.7432 (p0) REVERT: C 1304 MET cc_start: 0.8754 (tpp) cc_final: 0.8515 (tpp) REVERT: D 157 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8208 (pm20) REVERT: D 644 MET cc_start: 0.8777 (ptp) cc_final: 0.8358 (ptp) REVERT: D 869 CYS cc_start: 0.8554 (t) cc_final: 0.8165 (t) REVERT: D 1040 MET cc_start: 0.4652 (pmm) cc_final: 0.4229 (pmm) REVERT: E 55 GLU cc_start: 0.7174 (pp20) cc_final: 0.6436 (pp20) REVERT: E 71 GLU cc_start: 0.9105 (tt0) cc_final: 0.8669 (tm-30) REVERT: F 141 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7341 (mt) REVERT: F 286 LEU cc_start: 0.3580 (OUTLIER) cc_final: 0.3183 (pp) REVERT: F 322 MET cc_start: 0.6522 (tpt) cc_final: 0.4118 (ptt) REVERT: F 474 MET cc_start: 0.6984 (tpp) cc_final: 0.6451 (mmp) REVERT: F 489 MET cc_start: 0.5012 (ptp) cc_final: 0.2747 (ttt) outliers start: 61 outliers final: 42 residues processed: 231 average time/residue: 0.1614 time to fit residues: 63.5850 Evaluate side-chains 225 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 43 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 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 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 242 VAL Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 492 MET 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 843 THR 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 157 GLN Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 400 MET 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 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 480 PRO Chi-restraints excluded: chain F residue 483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [74, 114, 89, 26, 290, 240, 235, 83, 230, 271, 212] chunk 74 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 290 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 230 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN C1313 HIS ** D1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** 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 = 0.3762 r_free = 0.3762 target = 0.110384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.081478 restraints weight = 73530.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.079780 restraints weight = 67543.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080848 restraints weight = 67818.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.080917 restraints weight = 46015.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081466 restraints weight = 41650.053| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4242 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= 0.192 Angle : 0.651 13.999 41481 Z= 0.342 Chirality : 0.044 0.262 4725 Planarity : 0.004 0.044 5115 Dihedral : 14.974 138.599 4940 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.84 % Allowed : 17.17 % 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: -0.01 (0.14), residues: 3539 helix: 1.23 (0.14), residues: 1445 sheet: 0.03 (0.27), residues: 358 loop : -1.10 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 69 TYR 0.020 0.002 TYR C 291 PHE 0.018 0.002 PHE D 437 TRP 0.042 0.002 TRP C 997 HIS 0.008 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (30448) covalent geometry : angle 0.65142 / 0.34 (41481) hydrogen bonds : bond 0.04799 / 5.43 ( 1331) hydrogen bonds : angle 4.42199 / 5.06 ( 3750) metal coordination : bond 0.00602 / 0.30 ( 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 236 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 179 time to evaluate : 1.044 Fit side-chains revert: symmetry clash Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6335 (pm20) REVERT: A 185 TYR cc_start: 0.9049 (p90) cc_final: 0.8838 (p90) REVERT: C 185 ASP cc_start: 0.8105 (t70) cc_final: 0.7563 (t0) REVERT: C 242 VAL cc_start: 0.7990 (OUTLIER) cc_final: 0.7742 (p) REVERT: C 341 LEU cc_start: 0.6875 (pt) cc_final: 0.6372 (mm) REVERT: C 635 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.8998 (p) REVERT: D 157 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: D 869 CYS cc_start: 0.8627 (t) cc_final: 0.8253 (t) REVERT: E 55 GLU cc_start: 0.7153 (pp20) cc_final: 0.6407 (pp20) REVERT: E 71 GLU cc_start: 0.9115 (tt0) cc_final: 0.8712 (tm-30) REVERT: F 141 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7727 (mt) REVERT: F 273 MET cc_start: 0.7705 (mmm) cc_final: 0.7367 (mmt) REVERT: F 286 LEU cc_start: 0.4035 (OUTLIER) cc_final: 0.3681 (pp) REVERT: F 322 MET cc_start: 0.6523 (tpt) cc_final: 0.4115 (ptt) REVERT: F 365 MET cc_start: 0.8407 (ppp) cc_final: 0.8189 (ppp) REVERT: F 489 MET cc_start: 0.4792 (ptp) cc_final: 0.2767 (ttt) outliers start: 57 outliers final: 44 residues processed: 225 average time/residue: 0.1704 time to fit residues: 65.5545 Evaluate side-chains 223 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 43 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 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 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 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 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 157 GLN Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 400 MET 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 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 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 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: [298, 256, 350, 39, 322, 59, 255, 35, 210, 21, 349] chunk 298 optimal weight: 30.0000 chunk 256 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 322 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 349 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 153 ASN ** 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 = 0.3756 r_free = 0.3756 target = 0.109900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081228 restraints weight = 73271.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079581 restraints weight = 71372.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.080571 restraints weight = 64959.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.081063 restraints weight = 45183.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.081289 restraints weight = 42790.970| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4567 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= 0.176 Angle : 0.628 14.830 41481 Z= 0.325 Chirality : 0.044 0.331 4725 Planarity : 0.004 0.044 5115 Dihedral : 15.036 139.261 4940 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.81 % Allowed : 17.46 % Favored : 80.73 % 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: -0.02 (0.14), residues: 3539 helix: 1.26 (0.14), residues: 1440 sheet: 0.03 (0.27), residues: 350 loop : -1.13 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1216 TYR 0.023 0.001 TYR C 291 PHE 0.014 0.001 PHE D 437 TRP 0.036 0.002 TRP C 997 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (30448) covalent geometry : angle 0.62805 / 0.32 (41481) hydrogen bonds : bond 0.04532 / 5.13 ( 1331) hydrogen bonds : angle 4.36250 / 4.98 ( 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 237 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.877 Fit side-chains revert: symmetry clash Corrupt residue: chain: F residue: PRO 480 >>> skipping REVERT: A 7 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.6326 (pm20) REVERT: B 62 ASP cc_start: 0.6063 (p0) cc_final: 0.5696 (m-30) REVERT: C 124 MET cc_start: 0.8688 (ptp) cc_final: 0.8315 (ptp) REVERT: C 185 ASP cc_start: 0.8118 (t70) cc_final: 0.7661 (t0) REVERT: C 242 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7621 (p) REVERT: C 341 LEU cc_start: 0.6936 (pt) cc_final: 0.6461 (mm) REVERT: C 635 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.8949 (p) REVERT: D 157 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: D 404 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: D 869 CYS cc_start: 0.8599 (t) cc_final: 0.8239 (t) REVERT: E 55 GLU cc_start: 0.7122 (pp20) cc_final: 0.6364 (pp20) REVERT: E 69 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7917 (tpp80) REVERT: E 71 GLU cc_start: 0.9163 (tt0) cc_final: 0.8755 (tm-30) REVERT: E 72 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7246 (tm-30) REVERT: E 73 GLN cc_start: 0.7309 (pm20) cc_final: 0.6519 (pm20) REVERT: F 141 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7687 (mt) REVERT: F 273 MET cc_start: 0.7693 (mmm) cc_final: 0.7342 (mmt) REVERT: F 286 LEU cc_start: 0.3665 (OUTLIER) cc_final: 0.3238 (pp) REVERT: F 322 MET cc_start: 0.6603 (tpt) cc_final: 0.4166 (ptt) REVERT: F 365 MET cc_start: 0.8359 (ppp) cc_final: 0.8004 (ppp) REVERT: F 489 MET cc_start: 0.4775 (ptp) cc_final: 0.2814 (ttt) outliers start: 56 outliers final: 46 residues processed: 226 average time/residue: 0.1614 time to fit residues: 63.2953 Evaluate side-chains 222 residues out of total 3043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 169 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 43 LEU 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 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 131 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 232 ILE 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 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 843 THR 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 157 GLN 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 400 MET Chi-restraints excluded: chain D residue 404 GLU 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 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 480 PRO Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: [353, 310, 270, 246, 254, 41, 21, 154, 133, 218, 74] chunk 353 optimal weight: 10.0000 chunk 310 optimal weight: 0.0070 chunk 270 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 21 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN ** 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 = 0.3774 r_free = 0.3774 target = 0.111072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082606 restraints weight = 73750.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080792 restraints weight = 72631.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.081875 restraints weight = 64373.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082331 restraints weight = 44360.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.082610 restraints weight = 42025.256| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30450 Z= 0.118 Angle : 0.587 12.805 41481 Z= 0.305 Chirality : 0.043 0.294 4725 Planarity : 0.004 0.044 5115 Dihedral : 15.017 138.176 4940 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.87 % Allowed : 17.49 % Favored : 80.63 % 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: 1.39 (0.14), residues: 1439 sheet: 0.19 (0.28), residues: 340 loop : -1.06 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 150 TYR 0.036 0.001 TYR C 291 PHE 0.011 0.001 PHE C 405 TRP 0.090 0.003 TRP F 315 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (30448) covalent geometry : angle 0.58741 / 0.31 (41481) hydrogen bonds : bond 0.04083 / 4.65 ( 1331) hydrogen bonds : angle 4.22979 / 4.84 ( 3750) metal coordination : bond 0.00150 / 0.07 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4072.18 seconds wall clock time: 71 minutes 21.09 seconds (4281.09 seconds total)