Starting phenix.real_space_refine on Sun Jul 5 14:48:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m7y_63697/07_2026/9m7y_63697.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m7y_63697/07_2026/9m7y_63697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m7y_63697/07_2026/9m7y_63697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m7y_63697/07_2026/9m7y_63697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m7y_63697/07_2026/9m7y_63697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m7y_63697/07_2026/9m7y_63697.map" } resolution = 3.4 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 119 5.16 5 C 17376 2.51 5 N 4956 2.21 5 O 5582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28130 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Chain: "B" Number of atoms: 9133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1167, 9133 Classifications: {'peptide': 1167} Link IDs: {'PCIS': 2, 'PTRANS': 45, 'TRANS': 1119} Chain breaks: 1 Chain: "C" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "D" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1683 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Chain: "E" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 573 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "F" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1775 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "G" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 629 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "H" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1138 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain: "I" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 854 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain breaks: 1 Time building chain proxies: 5.78, per 1000 atoms: 0.21 Number of scatterers: 28130 At special positions: 0 Unit cell: (143.99, 154.7, 149.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 119 16.00 P 97 15.00 O 5582 8.00 N 4956 7.00 C 17376 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: 2.71 Conformation dependent library (CDL) restraints added in 997.4 milliseconds 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6142 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 43 sheets defined 45.0% alpha, 17.1% beta 41 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 4.15 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.982A pdb=" N ARG A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.639A pdb=" N SER A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.671A pdb=" N VAL A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 216 through 225 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 288 through 293 removed outlier: 3.520A pdb=" N ALA A 293 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 358 through 371 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.761A pdb=" N PHE A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 409 Processing helix chain 'A' and resid 421 through 438 Processing helix chain 'A' and resid 455 through 482 removed outlier: 3.858A pdb=" N ALA A 474 " --> pdb=" O ARG A 470 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.599A pdb=" N MET A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 509 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.714A pdb=" N ARG A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.681A pdb=" N TYR A 555 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 4.299A pdb=" N ASN A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 569 " --> pdb=" O GLY A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 608 through 612 removed outlier: 3.911A pdb=" N GLY A 612 " --> pdb=" O ALA A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 608 through 612' Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 675 through 686 Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 704 through 713 removed outlier: 3.833A pdb=" N GLY A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.857A pdb=" N ASP A 814 " --> pdb=" O ASN A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 826 Processing helix chain 'A' and resid 858 through 863 Processing helix chain 'A' and resid 896 through 906 removed outlier: 3.909A pdb=" N ILE A 905 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 983 Processing helix chain 'A' and resid 985 through 992 Processing helix chain 'A' and resid 995 through 1000 removed outlier: 4.036A pdb=" N GLU A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A1000 " --> pdb=" O ARG A 996 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 995 through 1000' Processing helix chain 'A' and resid 1004 through 1038 Processing helix chain 'A' and resid 1081 through 1085 Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 3.609A pdb=" N GLY A1102 " --> pdb=" O ASN A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1134 Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.504A pdb=" N LEU A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1177 Processing helix chain 'A' and resid 1191 through 1202 Processing helix chain 'A' and resid 1238 through 1243 Processing helix chain 'A' and resid 1271 through 1282 Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1297 through 1311 Processing helix chain 'A' and resid 1320 through 1333 removed outlier: 3.646A pdb=" N ASN A1324 " --> pdb=" O PRO A1320 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 4.030A pdb=" N LYS B 9 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 10 " --> pdb=" O LYS B 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5 through 11' Processing helix chain 'B' and resid 26 through 33 Processing helix chain 'B' and resid 58 through 63 removed outlier: 3.544A pdb=" N PHE B 62 " --> pdb=" O CYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 113 through 119 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 161 through 173 Processing helix chain 'B' and resid 181 through 192 Processing helix chain 'B' and resid 193 through 208 Processing helix chain 'B' and resid 210 through 231 removed outlier: 3.763A pdb=" N GLY B 231 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 263 through 285 removed outlier: 3.886A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 308 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 393 through 403 Processing helix chain 'B' and resid 405 through 417 removed outlier: 3.631A pdb=" N TRP B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 450 through 458 removed outlier: 4.042A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 504 through 515 Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 574 through 580 Processing helix chain 'B' and resid 588 through 592 removed outlier: 3.515A pdb=" N ILE B 591 " --> pdb=" O PRO B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 613 Processing helix chain 'B' and resid 613 through 636 removed outlier: 3.686A pdb=" N THR B 617 " --> pdb=" O GLY B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 644 Processing helix chain 'B' and resid 648 through 670 removed outlier: 4.441A pdb=" N GLU B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 702 Processing helix chain 'B' and resid 720 through 728 Processing helix chain 'B' and resid 733 through 742 removed outlier: 3.747A pdb=" N GLN B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 805 removed outlier: 3.830A pdb=" N HIS B 777 " --> pdb=" O PHE B 773 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY B 778 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA B 791 " --> pdb=" O ALA B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 840 Processing helix chain 'B' and resid 865 through 875 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 896 through 900 Processing helix chain 'B' and resid 914 through 925 Processing helix chain 'B' and resid 926 through 929 Processing helix chain 'B' and resid 1137 through 1147 Processing helix chain 'B' and resid 1216 through 1225 Processing helix chain 'B' and resid 1225 through 1243 removed outlier: 3.814A pdb=" N VAL B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1249 through 1261 removed outlier: 4.222A pdb=" N ILE B1253 " --> pdb=" O ASN B1249 " (cutoff:3.500A) Processing helix chain 'B' and resid 1282 through 1296 Processing helix chain 'B' and resid 1308 through 1315 Processing helix chain 'B' and resid 1318 through 1326 Processing helix chain 'B' and resid 1327 through 1339 Processing helix chain 'B' and resid 1346 through 1354 removed outlier: 3.555A pdb=" N ASN B1350 " --> pdb=" O GLY B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1360 through 1371 removed outlier: 3.897A pdb=" N ALA B1364 " --> pdb=" O GLY B1360 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR B1365 " --> pdb=" O THR B1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 removed outlier: 3.929A pdb=" N THR C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.898A pdb=" N HIS C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 233 removed outlier: 4.121A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 50 removed outlier: 3.516A pdb=" N THR D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 87 Processing helix chain 'D' and resid 113 through 115 No H-bonds generated for 'chain 'D' and resid 113 through 115' Processing helix chain 'D' and resid 212 through 229 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 56 Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'F' and resid 6 through 12 Processing helix chain 'F' and resid 22 through 43 removed outlier: 4.670A pdb=" N LYS F 32 " --> pdb=" O LYS F 28 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 63 Processing helix chain 'F' and resid 76 through 103 Processing helix chain 'F' and resid 121 through 130 removed outlier: 3.575A pdb=" N ILE F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 153 Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 170 through 179 Processing helix chain 'F' and resid 181 through 192 Processing helix chain 'F' and resid 192 through 204 Processing helix chain 'F' and resid 205 through 210 Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 58 removed outlier: 3.503A pdb=" N ARG G 57 " --> pdb=" O THR G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.295A pdb=" N LYS A 13 " --> pdb=" O ALA A1183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 5.562A pdb=" N SER A 66 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 105 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU A 68 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 103 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR A 70 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ARG A 101 " --> pdb=" O TYR A 70 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER A 72 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY A 125 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 98 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR A 123 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 100 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU A 121 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU A 102 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU A 119 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE A 104 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE A 117 " --> pdb=" O ILE A 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 454 removed outlier: 6.276A pdb=" N SER A 147 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 159 removed outlier: 5.151A pdb=" N TYR A 172 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 286 removed outlier: 4.788A pdb=" N ILE A 229 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 255 through 257 removed outlier: 6.650A pdb=" N ILE A 255 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA9, first strand: chain 'A' and resid 580 through 581 removed outlier: 5.577A pdb=" N GLU A 602 " --> pdb=" O LYS A 593 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR A 595 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR A 600 " --> pdb=" O THR A 595 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 580 through 581 Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 717 removed outlier: 6.327A pdb=" N ALA A 716 " --> pdb=" O LEU A 783 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.677A pdb=" N ARG A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 727 " --> pdb=" O ARG A 731 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 733 " --> pdb=" O GLN A 725 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 757 through 758 Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1209 through 1210 removed outlier: 7.108A pdb=" N ILE A 816 " --> pdb=" O LYS A1078 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASN A1080 " --> pdb=" O ILE A 816 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 818 " --> pdb=" O ASN A1080 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 817 " --> pdb=" O VAL A1097 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ILE A1096 " --> pdb=" O ASN A 799 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG A 801 " --> pdb=" O ILE A1096 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU A1098 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 803 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR A1226 " --> pdb=" O PHE A 804 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 846 through 847 removed outlier: 6.257A pdb=" N ASP A 842 " --> pdb=" O VAL A1046 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A1046 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP A 930 " --> pdb=" O TYR A1053 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A1055 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL A 928 " --> pdb=" O ALA A1055 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LYS A1057 " --> pdb=" O GLY A 926 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLY A 926 " --> pdb=" O LYS A1057 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 882 through 884 removed outlier: 6.643A pdb=" N LEU A 918 " --> pdb=" O LEU A 883 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 887 through 889 Processing sheet with id=AC1, first strand: chain 'A' and resid 1244 through 1246 removed outlier: 7.669A pdb=" N ILE B 447 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 354 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 449 " --> pdb=" O VAL B 354 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR B 356 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1268 through 1270 removed outlier: 3.706A pdb=" N GLN A1268 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1335 through 1340 Processing sheet with id=AC4, first strand: chain 'B' and resid 34 through 37 removed outlier: 7.631A pdb=" N HIS B 104 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 37 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLU B 106 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N LEU B 107 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 10.362A pdb=" N SER B 109 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 241 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 160 removed outlier: 7.067A pdb=" N ASP B 177 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 252 through 254 Processing sheet with id=AC7, first strand: chain 'B' and resid 526 through 527 Processing sheet with id=AC8, first strand: chain 'B' and resid 703 through 707 Processing sheet with id=AC9, first strand: chain 'B' and resid 809 through 811 Processing sheet with id=AD1, first strand: chain 'B' and resid 820 through 822 Processing sheet with id=AD2, first strand: chain 'B' and resid 825 through 827 removed outlier: 6.875A pdb=" N GLU B 827 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL B 831 " --> pdb=" O GLU B 827 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 848 through 849 Processing sheet with id=AD4, first strand: chain 'B' and resid 1155 through 1156 removed outlier: 6.435A pdb=" N ILE B1155 " --> pdb=" O ILE B1210 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1186 through 1191 Processing sheet with id=AD6, first strand: chain 'B' and resid 1279 through 1281 removed outlier: 6.637A pdb=" N THR B1301 " --> pdb=" O VAL B1267 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 12 through 18 removed outlier: 4.871A pdb=" N LEU C 13 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU C 29 " --> pdb=" O LEU C 13 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP C 15 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N HIS C 23 " --> pdb=" O THR C 207 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N THR C 207 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS C 25 " --> pdb=" O MET C 205 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET C 205 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR C 27 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE C 203 " --> pdb=" O THR C 27 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLU C 29 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU C 201 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 192 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 198 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.635A pdb=" N THR C 101 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 58 " --> pdb=" O LYS C 145 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLN C 147 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL C 56 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY C 149 " --> pdb=" O CYS C 54 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N CYS C 54 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 90 through 92 Processing sheet with id=AE1, first strand: chain 'C' and resid 108 through 111 removed outlier: 6.547A pdb=" N GLY C 108 " --> pdb=" O HIS C 132 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N HIS C 132 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL C 110 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 152 through 153 Processing sheet with id=AE3, first strand: chain 'D' and resid 12 through 20 removed outlier: 4.866A pdb=" N LEU D 13 " --> pdb=" O GLU D 29 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLU D 29 " --> pdb=" O LEU D 13 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP D 15 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP D 199 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP D 197 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ALA D 190 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP D 199 " --> pdb=" O GLU D 188 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU D 188 " --> pdb=" O ASP D 199 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU D 201 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASN D 186 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE D 203 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA D 184 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET D 205 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG D 182 " --> pdb=" O MET D 205 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 207 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL D 180 " --> pdb=" O THR D 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 97 through 105 removed outlier: 7.845A pdb=" N SER D 141 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE D 61 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG D 143 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL D 59 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS D 145 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 90 through 92 Processing sheet with id=AE6, first strand: chain 'D' and resid 108 through 111 removed outlier: 6.419A pdb=" N GLY D 108 " --> pdb=" O HIS D 132 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS D 132 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL D 110 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 152 through 153 1230 hydrogen bonds defined for protein. 3498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4809 1.32 - 1.44: 7354 1.44 - 1.57: 16215 1.57 - 1.69: 192 1.69 - 1.81: 208 Bond restraints: 28778 Sorted by residual: bond pdb=" C PRO A 375 " pdb=" N PRO A 376 " ideal model delta sigma weight residual 1.335 1.365 -0.030 8.70e-03 1.32e+04 1.20e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" N THR B 514 " pdb=" CA THR B 514 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.32e-02 5.74e+03 1.04e+01 bond pdb=" C3' DC H 51 " pdb=" C2' DC H 51 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C ILE F 169 " pdb=" N PRO F 170 " ideal model delta sigma weight residual 1.332 1.374 -0.043 1.33e-02 5.65e+03 1.03e+01 ... (remaining 28773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 38524 2.35 - 4.71: 671 4.71 - 7.06: 57 7.06 - 9.42: 13 9.42 - 11.77: 2 Bond angle restraints: 39267 Sorted by residual: angle pdb=" C PRO F 170 " pdb=" CA PRO F 170 " pdb=" CB PRO F 170 " ideal model delta sigma weight residual 111.39 103.27 8.12 1.28e+00 6.10e-01 4.02e+01 angle pdb=" N PRO B 251 " pdb=" CA PRO B 251 " pdb=" C PRO B 251 " ideal model delta sigma weight residual 111.38 121.28 -9.90 1.59e+00 3.96e-01 3.87e+01 angle pdb=" C TYR D 177 " pdb=" N SER D 178 " pdb=" CA SER D 178 " ideal model delta sigma weight residual 120.65 128.35 -7.70 1.36e+00 5.41e-01 3.21e+01 angle pdb=" N ASN G 12 " pdb=" CA ASN G 12 " pdb=" C ASN G 12 " ideal model delta sigma weight residual 113.16 107.02 6.14 1.24e+00 6.50e-01 2.45e+01 angle pdb=" C PRO D 179 " pdb=" CA PRO D 179 " pdb=" CB PRO D 179 " ideal model delta sigma weight residual 111.56 104.13 7.43 1.65e+00 3.67e-01 2.03e+01 ... (remaining 39262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 16505 35.77 - 71.54: 925 71.54 - 107.31: 31 107.31 - 143.08: 1 143.08 - 178.85: 2 Dihedral angle restraints: 17464 sinusoidal: 7922 harmonic: 9542 Sorted by residual: dihedral pdb=" CA GLN G 47 " pdb=" C GLN G 47 " pdb=" N PHE G 48 " pdb=" CA PHE G 48 " ideal model delta harmonic sigma weight residual 180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C PRO F 170 " pdb=" N PRO F 170 " pdb=" CA PRO F 170 " pdb=" CB PRO F 170 " ideal model delta harmonic sigma weight residual -120.70 -110.29 -10.41 0 2.50e+00 1.60e-01 1.73e+01 dihedral pdb=" CA ASP B 878 " pdb=" C ASP B 878 " pdb=" N ALA B 879 " pdb=" CA ALA B 879 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 17461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3564 0.060 - 0.121: 786 0.121 - 0.181: 66 0.181 - 0.241: 14 0.241 - 0.302: 5 Chirality restraints: 4435 Sorted by residual: chirality pdb=" CA ILE F 169 " pdb=" N ILE F 169 " pdb=" C ILE F 169 " pdb=" CB ILE F 169 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA LEU G 6 " pdb=" N LEU G 6 " pdb=" C LEU G 6 " pdb=" CB LEU G 6 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA LEU B 252 " pdb=" N LEU B 252 " pdb=" C LEU B 252 " pdb=" CB LEU B 252 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4432 not shown) Planarity restraints: 4796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.066 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO A 205 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 75 " -0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" CD GLN C 75 " 0.062 2.00e-02 2.50e+03 pdb=" OE1 GLN C 75 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN C 75 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 139 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C GLU F 139 " -0.052 2.00e-02 2.50e+03 pdb=" O GLU F 139 " 0.019 2.00e-02 2.50e+03 pdb=" N SER F 140 " 0.017 2.00e-02 2.50e+03 ... (remaining 4793 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 296 2.61 - 3.18: 23650 3.18 - 3.75: 44795 3.75 - 4.33: 62505 4.33 - 4.90: 102319 Nonbonded interactions: 233565 Sorted by model distance: nonbonded pdb=" NH2 ARG B 417 " pdb=" OE2 GLU B 418 " model vdw 2.035 3.120 nonbonded pdb=" OD1 ASP G 76 " pdb=" N LYS G 77 " model vdw 2.184 3.120 nonbonded pdb=" OG1 THR B 890 " pdb=" O GLY B 893 " model vdw 2.196 3.040 nonbonded pdb=" OG SER A 93 " pdb=" OE1 GLU A 126 " model vdw 2.202 3.040 nonbonded pdb=" N GLU B1158 " pdb=" OE1 GLU B1158 " model vdw 2.215 3.120 ... (remaining 233560 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 'C' and (resid 7 through 158 or resid 170 through 232)) selection = (chain 'D' and resid 7 through 232) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.490 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 : 0.008 0.105 28778 Z= 0.394 Angle : 0.761 11.769 39267 Z= 0.495 Chirality : 0.050 0.302 4435 Planarity : 0.005 0.098 4796 Dihedral : 18.911 178.852 11322 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.28 % Favored : 97.63 % Rotamer: Outliers : 0.81 % Allowed : 16.95 % Favored : 82.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.85 % 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: 0.50 (0.14), residues: 3294 helix: 1.05 (0.14), residues: 1316 sheet: -0.39 (0.24), residues: 396 loop : 0.04 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 151 TYR 0.023 0.002 TYR B 140 PHE 0.031 0.003 PHE B 17 TRP 0.013 0.002 TRP F 90 HIS 0.010 0.002 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.39 (28778) covalent geometry : angle 0.76147 / 0.49 (39267) hydrogen bonds : bond 0.13621 / 8.81 ( 1320) hydrogen bonds : angle 6.30186 / 4.42 ( 3682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 MET cc_start: 0.6344 (tpt) cc_final: 0.5985 (tpt) outliers start: 23 outliers final: 6 residues processed: 226 average time/residue: 0.1986 time to fit residues: 68.9545 Evaluate side-chains 147 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 893 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 798 GLN A1070 HIS ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN C 132 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.041130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.030909 restraints weight = 185767.027| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 4.12 r_work: 0.2748 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 28778 Z= 0.240 Angle : 0.640 8.762 39267 Z= 0.343 Chirality : 0.043 0.268 4435 Planarity : 0.005 0.078 4796 Dihedral : 17.492 178.512 4759 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 2.04 % Allowed : 17.02 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.82 (0.14), residues: 3294 helix: 1.48 (0.14), residues: 1351 sheet: -0.41 (0.23), residues: 427 loop : 0.09 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 275 TYR 0.019 0.001 TYR B 140 PHE 0.015 0.002 PHE B 141 TRP 0.008 0.001 TRP F 60 HIS 0.005 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (28778) covalent geometry : angle 0.63950 / 0.34 (39267) hydrogen bonds : bond 0.04689 / 3.12 ( 1320) hydrogen bonds : angle 5.03080 / 3.56 ( 3682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 150 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 MET cc_start: 0.9379 (mpp) cc_final: 0.9169 (mpp) REVERT: A 479 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9050 (tp) REVERT: A 704 MET cc_start: 0.8148 (mmp) cc_final: 0.7873 (mmt) REVERT: A 800 MET cc_start: 0.8477 (mmm) cc_final: 0.8168 (mmm) REVERT: A 909 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8205 (tppt) REVERT: A 1319 MET cc_start: 0.9201 (tpp) cc_final: 0.8686 (tpp) REVERT: B 162 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8377 (pp20) REVERT: B 466 MET cc_start: 0.8794 (mtp) cc_final: 0.8422 (ttt) REVERT: B 644 MET cc_start: 0.9140 (mtm) cc_final: 0.8817 (mtm) REVERT: D 125 LYS cc_start: 0.9204 (tppt) cc_final: 0.8997 (tptt) REVERT: F 77 ASP cc_start: 0.9350 (OUTLIER) cc_final: 0.8980 (m-30) REVERT: F 81 MET cc_start: 0.8839 (tmm) cc_final: 0.8577 (tmm) REVERT: G 14 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7661 (tmm) REVERT: G 16 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7564 (pp20) REVERT: G 18 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7278 (mttt) outliers start: 58 outliers final: 17 residues processed: 200 average time/residue: 0.1737 time to fit residues: 56.0449 Evaluate side-chains 161 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 308 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 282 optimal weight: 40.0000 chunk 39 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 241 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 265 optimal weight: 30.0000 chunk 206 optimal weight: 3.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 554 HIS A 856 ASN ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 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 = 0.3324 r_free = 0.3324 target = 0.040677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.030596 restraints weight = 187045.844| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.11 r_work: 0.2745 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28778 Z= 0.196 Angle : 0.588 9.711 39267 Z= 0.314 Chirality : 0.042 0.265 4435 Planarity : 0.004 0.073 4796 Dihedral : 17.453 177.836 4757 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.33 % Rotamer: Outliers : 1.93 % Allowed : 16.91 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.96 (0.15), residues: 3294 helix: 1.67 (0.14), residues: 1340 sheet: -0.35 (0.23), residues: 426 loop : 0.10 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 52 TYR 0.016 0.001 TYR B 723 PHE 0.016 0.002 PHE B 172 TRP 0.008 0.001 TRP G 36 HIS 0.007 0.001 HIS D 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (28778) covalent geometry : angle 0.58772 / 0.31 (39267) hydrogen bonds : bond 0.04245 / 2.79 ( 1320) hydrogen bonds : angle 4.75220 / 3.36 ( 3682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8728 (tmm) cc_final: 0.8482 (tmm) REVERT: A 429 MET cc_start: 0.9402 (mpp) cc_final: 0.9004 (mpp) REVERT: A 488 MET cc_start: 0.9412 (mmm) cc_final: 0.9150 (tmm) REVERT: A 510 GLN cc_start: 0.9453 (OUTLIER) cc_final: 0.9125 (tp-100) REVERT: A 704 MET cc_start: 0.8207 (mmp) cc_final: 0.7947 (mmt) REVERT: A 800 MET cc_start: 0.8542 (mmm) cc_final: 0.8229 (mmm) REVERT: A 909 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8053 (tppt) REVERT: A 1243 MET cc_start: 0.9332 (tmm) cc_final: 0.9020 (tmm) REVERT: A 1341 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7632 (t0) REVERT: B 330 MET cc_start: 0.9102 (mtp) cc_final: 0.8862 (mtm) REVERT: B 644 MET cc_start: 0.9129 (mtm) cc_final: 0.8558 (mtm) REVERT: B 698 MET cc_start: 0.9163 (tpp) cc_final: 0.8424 (tmm) REVERT: B 932 MET cc_start: 0.6587 (mtm) cc_final: 0.6381 (mtm) REVERT: B 1189 MET cc_start: 0.9066 (tpp) cc_final: 0.8821 (tpp) REVERT: E 67 ARG cc_start: 0.8961 (tpp-160) cc_final: 0.8624 (tpp-160) REVERT: F 81 MET cc_start: 0.8926 (tmm) cc_final: 0.8620 (tmm) REVERT: F 120 ASP cc_start: 0.8260 (OUTLIER) cc_final: 0.7920 (p0) REVERT: F 157 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9282 (tttt) REVERT: F 206 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8938 (tptt) REVERT: G 14 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7482 (tmm) REVERT: G 16 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7002 (pp20) outliers start: 55 outliers final: 25 residues processed: 192 average time/residue: 0.1741 time to fit residues: 54.1297 Evaluate side-chains 163 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain G residue 14 MET Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 262 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 240 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 387 ASN A1111 GLN ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN F 182 HIS ** G 40 ASN ** 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 = 0.3285 r_free = 0.3285 target = 0.039553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.029761 restraints weight = 191192.790| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.91 r_work: 0.2726 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 28778 Z= 0.259 Angle : 0.614 8.246 39267 Z= 0.327 Chirality : 0.043 0.264 4435 Planarity : 0.004 0.071 4796 Dihedral : 17.480 177.404 4752 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 2.25 % Allowed : 17.41 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.88 (0.14), residues: 3294 helix: 1.59 (0.14), residues: 1345 sheet: -0.29 (0.23), residues: 428 loop : 0.04 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 81 TYR 0.018 0.001 TYR B 723 PHE 0.018 0.002 PHE B 172 TRP 0.007 0.001 TRP F 60 HIS 0.006 0.001 HIS B 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.26 (28778) covalent geometry : angle 0.61427 / 0.33 (39267) hydrogen bonds : bond 0.04463 / 2.94 ( 1320) hydrogen bonds : angle 4.76757 / 3.36 ( 3682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9036 (mm) REVERT: A 429 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9054 (mpp) REVERT: A 488 MET cc_start: 0.9358 (mmm) cc_final: 0.9135 (mmm) REVERT: A 510 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9207 (tp-100) REVERT: A 704 MET cc_start: 0.8318 (mmp) cc_final: 0.7975 (mmt) REVERT: A 909 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8093 (tppt) REVERT: A 1119 MET cc_start: 0.8541 (ttp) cc_final: 0.8329 (ttp) REVERT: A 1341 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7958 (t0) REVERT: B 102 MET cc_start: 0.8952 (mtm) cc_final: 0.8738 (mtm) REVERT: B 137 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8718 (ttm110) REVERT: B 443 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8551 (mm-30) REVERT: B 466 MET cc_start: 0.8632 (ttp) cc_final: 0.8407 (ttm) REVERT: B 644 MET cc_start: 0.9034 (mtm) cc_final: 0.8394 (mtm) REVERT: B 698 MET cc_start: 0.9100 (tpp) cc_final: 0.8378 (tmm) REVERT: B 822 MET cc_start: 0.8984 (tpp) cc_final: 0.8759 (tpp) REVERT: B 1189 MET cc_start: 0.9043 (tpp) cc_final: 0.8813 (tpp) REVERT: E 67 ARG cc_start: 0.8938 (tpp-160) cc_final: 0.8689 (tpp-160) REVERT: F 81 MET cc_start: 0.9020 (tmm) cc_final: 0.8726 (tmm) REVERT: F 139 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8626 (pt0) outliers start: 64 outliers final: 34 residues processed: 187 average time/residue: 0.1684 time to fit residues: 51.0329 Evaluate side-chains 168 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 209 PHE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 6 optimal weight: 20.0000 chunk 283 optimal weight: 30.0000 chunk 181 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 322 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 240 optimal weight: 30.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN C 132 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN G 12 ASN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.039553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.029758 restraints weight = 190963.900| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.94 r_work: 0.2730 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28778 Z= 0.201 Angle : 0.584 9.620 39267 Z= 0.309 Chirality : 0.042 0.263 4435 Planarity : 0.004 0.071 4796 Dihedral : 17.437 176.653 4749 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 2.71 % Allowed : 17.37 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.98 (0.15), residues: 3294 helix: 1.69 (0.14), residues: 1338 sheet: -0.24 (0.24), residues: 428 loop : 0.09 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1177 TYR 0.015 0.001 TYR B 723 PHE 0.017 0.002 PHE F 146 TRP 0.006 0.001 TRP F 60 HIS 0.011 0.001 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (28778) covalent geometry : angle 0.58400 / 0.31 (39267) hydrogen bonds : bond 0.04142 / 2.72 ( 1320) hydrogen bonds : angle 4.66183 / 3.29 ( 3682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 129 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8858 (mt-10) REVERT: A 351 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9063 (mm) REVERT: A 429 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9060 (mpp) REVERT: A 488 MET cc_start: 0.9383 (mmm) cc_final: 0.9182 (mmm) REVERT: A 510 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.9198 (tp-100) REVERT: A 704 MET cc_start: 0.8315 (mmp) cc_final: 0.8025 (mmt) REVERT: A 909 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8164 (tppt) REVERT: A 1107 MET cc_start: 0.9540 (mtm) cc_final: 0.9335 (mtt) REVERT: A 1119 MET cc_start: 0.8539 (ttp) cc_final: 0.8318 (ttp) REVERT: A 1243 MET cc_start: 0.9284 (tmm) cc_final: 0.8976 (tmm) REVERT: A 1341 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.8020 (t0) REVERT: B 3 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8204 (t0) REVERT: B 102 MET cc_start: 0.8984 (mtm) cc_final: 0.8743 (mtm) REVERT: B 137 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8740 (ttm110) REVERT: B 443 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: B 644 MET cc_start: 0.9069 (mtm) cc_final: 0.8481 (mtm) REVERT: B 698 MET cc_start: 0.9089 (tpp) cc_final: 0.8356 (tmm) REVERT: B 822 MET cc_start: 0.9026 (tpp) cc_final: 0.8783 (tpp) REVERT: B 1189 MET cc_start: 0.9046 (tpp) cc_final: 0.8820 (tpp) REVERT: E 15 ASN cc_start: 0.7888 (t0) cc_final: 0.7399 (t0) REVERT: F 81 MET cc_start: 0.9054 (tmm) cc_final: 0.8750 (tmm) REVERT: F 115 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9115 (p) REVERT: F 139 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8576 (pt0) outliers start: 77 outliers final: 41 residues processed: 195 average time/residue: 0.1601 time to fit residues: 52.2758 Evaluate side-chains 180 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 972 PHE Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 144 optimal weight: 7.9990 chunk 233 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 249 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 190 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** G 40 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 = 0.3291 r_free = 0.3291 target = 0.039656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.029928 restraints weight = 189144.592| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.92 r_work: 0.2736 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28778 Z= 0.164 Angle : 0.563 10.190 39267 Z= 0.298 Chirality : 0.042 0.264 4435 Planarity : 0.004 0.069 4796 Dihedral : 17.378 175.941 4749 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 2.22 % Allowed : 18.28 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.08 (0.15), residues: 3294 helix: 1.76 (0.14), residues: 1341 sheet: -0.18 (0.24), residues: 428 loop : 0.15 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 52 TYR 0.013 0.001 TYR B 723 PHE 0.014 0.001 PHE B 172 TRP 0.006 0.001 TRP G 36 HIS 0.007 0.001 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (28778) covalent geometry : angle 0.56286 / 0.30 (39267) hydrogen bonds : bond 0.03992 / 2.63 ( 1320) hydrogen bonds : angle 4.58046 / 3.24 ( 3682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9078 (mm) REVERT: A 429 MET cc_start: 0.9394 (OUTLIER) cc_final: 0.9054 (mpp) REVERT: A 488 MET cc_start: 0.9359 (mmm) cc_final: 0.9146 (mmm) REVERT: A 510 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.9206 (tp-100) REVERT: A 704 MET cc_start: 0.8301 (mmp) cc_final: 0.8081 (mmt) REVERT: A 909 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8167 (tppt) REVERT: A 1119 MET cc_start: 0.8519 (ttp) cc_final: 0.8298 (ttp) REVERT: A 1243 MET cc_start: 0.9274 (tmm) cc_final: 0.8976 (tmm) REVERT: A 1341 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8023 (t0) REVERT: B 102 MET cc_start: 0.8952 (mtm) cc_final: 0.8701 (mtm) REVERT: B 137 ARG cc_start: 0.9372 (OUTLIER) cc_final: 0.8771 (ttm110) REVERT: B 443 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8508 (mm-30) REVERT: B 644 MET cc_start: 0.9033 (mtm) cc_final: 0.8368 (mtm) REVERT: B 698 MET cc_start: 0.9075 (tpp) cc_final: 0.8367 (tmm) REVERT: B 822 MET cc_start: 0.9074 (tpp) cc_final: 0.8746 (tpp) REVERT: B 1189 MET cc_start: 0.9049 (tpp) cc_final: 0.8837 (tpp) REVERT: D 9 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9096 (mp) REVERT: E 53 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8288 (mt-10) REVERT: F 81 MET cc_start: 0.9082 (tmm) cc_final: 0.8754 (tmm) REVERT: F 139 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8651 (pt0) outliers start: 63 outliers final: 42 residues processed: 187 average time/residue: 0.1769 time to fit residues: 54.9677 Evaluate side-chains 180 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 129 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 227 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1010 GLN ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 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 = 0.3278 r_free = 0.3278 target = 0.039311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.029637 restraints weight = 190666.836| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 3.88 r_work: 0.2720 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28778 Z= 0.201 Angle : 0.574 10.666 39267 Z= 0.304 Chirality : 0.042 0.266 4435 Planarity : 0.004 0.068 4796 Dihedral : 17.368 175.751 4749 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 2.29 % Allowed : 18.42 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.07 (0.15), residues: 3294 helix: 1.74 (0.14), residues: 1342 sheet: -0.14 (0.24), residues: 416 loop : 0.12 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 69 TYR 0.014 0.001 TYR B 723 PHE 0.015 0.001 PHE B 172 TRP 0.007 0.001 TRP B 33 HIS 0.030 0.001 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (28778) covalent geometry : angle 0.57355 / 0.30 (39267) hydrogen bonds : bond 0.04049 / 2.67 ( 1320) hydrogen bonds : angle 4.59546 / 3.24 ( 3682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9089 (mm) REVERT: A 429 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.9113 (mpp) REVERT: A 488 MET cc_start: 0.9384 (mmm) cc_final: 0.9171 (mmm) REVERT: A 510 GLN cc_start: 0.9503 (OUTLIER) cc_final: 0.9225 (tp-100) REVERT: A 704 MET cc_start: 0.8326 (mmp) cc_final: 0.8116 (mmt) REVERT: A 909 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8152 (tppt) REVERT: A 1119 MET cc_start: 0.8535 (ttp) cc_final: 0.8325 (ttp) REVERT: A 1243 MET cc_start: 0.9292 (tmm) cc_final: 0.9030 (tmm) REVERT: A 1341 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.8039 (t0) REVERT: B 3 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8159 (t0) REVERT: B 102 MET cc_start: 0.8974 (mtm) cc_final: 0.8728 (mtm) REVERT: B 130 MET cc_start: 0.8823 (tmm) cc_final: 0.8613 (tmm) REVERT: B 137 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8816 (ttm110) REVERT: B 443 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8548 (mm-30) REVERT: B 644 MET cc_start: 0.9042 (mtm) cc_final: 0.8364 (mtm) REVERT: B 698 MET cc_start: 0.9067 (tpp) cc_final: 0.8360 (tmm) REVERT: B 822 MET cc_start: 0.9124 (tpp) cc_final: 0.8799 (tpp) REVERT: D 9 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9122 (mp) REVERT: E 53 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8309 (mt-10) REVERT: F 81 MET cc_start: 0.9111 (tmm) cc_final: 0.8783 (tmm) REVERT: F 127 MET cc_start: 0.7475 (ttp) cc_final: 0.6724 (tmm) REVERT: F 139 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8667 (pt0) REVERT: F 180 MET cc_start: 0.9216 (ttp) cc_final: 0.8933 (ttp) outliers start: 65 outliers final: 43 residues processed: 191 average time/residue: 0.1819 time to fit residues: 57.2505 Evaluate side-chains 181 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 128 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 959 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 168 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 208 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1268 GLN ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** 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 = 0.3293 r_free = 0.3293 target = 0.039681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030025 restraints weight = 190701.234| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.91 r_work: 0.2742 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28778 Z= 0.138 Angle : 0.549 11.613 39267 Z= 0.291 Chirality : 0.041 0.265 4435 Planarity : 0.004 0.068 4796 Dihedral : 17.311 175.067 4749 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.36 % Rotamer: Outliers : 2.07 % Allowed : 18.85 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.17 (0.15), residues: 3294 helix: 1.85 (0.14), residues: 1341 sheet: -0.15 (0.24), residues: 437 loop : 0.20 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 42 TYR 0.013 0.001 TYR B 631 PHE 0.012 0.001 PHE B 172 TRP 0.008 0.001 TRP G 36 HIS 0.004 0.001 HIS D 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (28778) covalent geometry : angle 0.54889 / 0.29 (39267) hydrogen bonds : bond 0.03818 / 2.51 ( 1320) hydrogen bonds : angle 4.48947 / 3.18 ( 3682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 133 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8788 (mt-10) REVERT: A 351 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9094 (mm) REVERT: A 429 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.9077 (mpp) REVERT: A 488 MET cc_start: 0.9352 (mmm) cc_final: 0.9130 (mmm) REVERT: A 510 GLN cc_start: 0.9480 (OUTLIER) cc_final: 0.9189 (tp-100) REVERT: A 909 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8167 (tppt) REVERT: A 1107 MET cc_start: 0.9484 (mtm) cc_final: 0.8677 (mpp) REVERT: A 1119 MET cc_start: 0.8509 (ttp) cc_final: 0.8299 (ttp) REVERT: A 1341 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8037 (t0) REVERT: B 3 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8198 (t0) REVERT: B 130 MET cc_start: 0.8750 (tmm) cc_final: 0.8545 (tmm) REVERT: B 137 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.8859 (ttm110) REVERT: B 443 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8517 (mm-30) REVERT: B 644 MET cc_start: 0.9032 (mtm) cc_final: 0.8341 (mtm) REVERT: B 698 MET cc_start: 0.9011 (tpp) cc_final: 0.8264 (tmm) REVERT: B 822 MET cc_start: 0.9115 (tpp) cc_final: 0.8792 (tpp) REVERT: D 9 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9094 (mp) REVERT: E 53 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8145 (mt-10) REVERT: F 81 MET cc_start: 0.9079 (tmm) cc_final: 0.8749 (tmm) outliers start: 59 outliers final: 39 residues processed: 184 average time/residue: 0.1629 time to fit residues: 50.2685 Evaluate side-chains 180 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 131 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 299 optimal weight: 30.0000 chunk 171 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 331 optimal weight: 50.0000 chunk 214 optimal weight: 0.2980 chunk 187 optimal weight: 10.0000 chunk 207 optimal weight: 0.0170 chunk 174 optimal weight: 5.9990 chunk 100 optimal weight: 40.0000 overall best weight: 3.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 HIS ** F 35 HIS ** 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 = 0.3293 r_free = 0.3293 target = 0.039659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030004 restraints weight = 190455.454| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.90 r_work: 0.2741 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28778 Z= 0.142 Angle : 0.556 11.693 39267 Z= 0.294 Chirality : 0.041 0.266 4435 Planarity : 0.004 0.067 4796 Dihedral : 17.277 174.815 4749 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 1.90 % Allowed : 19.16 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.20 (0.15), residues: 3294 helix: 1.87 (0.14), residues: 1342 sheet: -0.11 (0.24), residues: 437 loop : 0.21 (0.16), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 69 TYR 0.012 0.001 TYR B 631 PHE 0.012 0.001 PHE B 172 TRP 0.015 0.001 TRP B 33 HIS 0.016 0.001 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (28778) covalent geometry : angle 0.55611 / 0.29 (39267) hydrogen bonds : bond 0.03783 / 2.49 ( 1320) hydrogen bonds : angle 4.47677 / 3.17 ( 3682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8791 (mt-10) REVERT: A 351 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9100 (mm) REVERT: A 429 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.9128 (mpp) REVERT: A 510 GLN cc_start: 0.9470 (OUTLIER) cc_final: 0.9183 (tp-100) REVERT: A 909 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8125 (tppt) REVERT: A 1107 MET cc_start: 0.9464 (mtm) cc_final: 0.8666 (mpp) REVERT: A 1119 MET cc_start: 0.8507 (ttp) cc_final: 0.8301 (ttp) REVERT: A 1341 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.8043 (t0) REVERT: B 3 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8209 (t0) REVERT: B 137 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8868 (ttm110) REVERT: B 372 MET cc_start: 0.9087 (mtp) cc_final: 0.8800 (mtt) REVERT: B 443 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8516 (mm-30) REVERT: B 644 MET cc_start: 0.9017 (mtm) cc_final: 0.8332 (mtm) REVERT: B 698 MET cc_start: 0.8988 (tpp) cc_final: 0.8236 (tmm) REVERT: B 822 MET cc_start: 0.9100 (tpp) cc_final: 0.8748 (tpp) REVERT: B 1260 MET cc_start: 0.8777 (mtt) cc_final: 0.8334 (mtt) REVERT: D 9 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9107 (mp) REVERT: E 53 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8235 (mt-10) REVERT: F 81 MET cc_start: 0.9090 (tmm) cc_final: 0.8760 (tmm) REVERT: F 180 MET cc_start: 0.9038 (ttp) cc_final: 0.8725 (ttp) REVERT: G 18 LYS cc_start: 0.6395 (mmtm) cc_final: 0.5356 (mttt) outliers start: 54 outliers final: 40 residues processed: 179 average time/residue: 0.1650 time to fit residues: 49.1343 Evaluate side-chains 180 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 231 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 16 optimal weight: 0.0040 chunk 239 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 317 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 overall best weight: 3.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.039514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.029876 restraints weight = 190672.191| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.92 r_work: 0.2733 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28778 Z= 0.149 Angle : 0.570 16.420 39267 Z= 0.299 Chirality : 0.041 0.264 4435 Planarity : 0.004 0.066 4796 Dihedral : 17.248 174.607 4749 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 1.90 % Allowed : 19.23 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.22 (0.15), residues: 3294 helix: 1.87 (0.14), residues: 1343 sheet: -0.04 (0.24), residues: 426 loop : 0.20 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.012 0.001 TYR B 723 PHE 0.012 0.001 PHE B 172 TRP 0.007 0.001 TRP G 36 HIS 0.011 0.001 HIS D 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (28778) covalent geometry : angle 0.57015 / 0.30 (39267) hydrogen bonds : bond 0.03780 / 2.47 ( 1320) hydrogen bonds : angle 4.47856 / 3.17 ( 3682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 132 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8812 (mt-10) REVERT: A 351 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9102 (mm) REVERT: A 429 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.9126 (mpp) REVERT: A 510 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.9169 (tp-100) REVERT: A 909 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8124 (tppt) REVERT: A 1107 MET cc_start: 0.9459 (mtm) cc_final: 0.8687 (mpp) REVERT: A 1119 MET cc_start: 0.8519 (ttp) cc_final: 0.8316 (ttp) REVERT: A 1341 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.8048 (t0) REVERT: B 3 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8182 (t0) REVERT: B 29 MET cc_start: 0.8217 (mmm) cc_final: 0.6985 (tpp) REVERT: B 137 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8760 (ttm110) REVERT: B 162 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8261 (pp20) REVERT: B 443 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8538 (mm-30) REVERT: B 644 MET cc_start: 0.8998 (mtm) cc_final: 0.8309 (mtm) REVERT: B 698 MET cc_start: 0.8972 (tpp) cc_final: 0.8215 (tmm) REVERT: B 822 MET cc_start: 0.9111 (tpp) cc_final: 0.8763 (tpp) REVERT: B 1260 MET cc_start: 0.8765 (mtt) cc_final: 0.8322 (mtt) REVERT: D 9 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9131 (mp) REVERT: E 53 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8152 (mt-10) REVERT: F 81 MET cc_start: 0.9101 (tmm) cc_final: 0.8788 (tmm) REVERT: F 180 MET cc_start: 0.8958 (ttp) cc_final: 0.8738 (ttp) REVERT: G 18 LYS cc_start: 0.6408 (mmtm) cc_final: 0.5411 (mttt) outliers start: 54 outliers final: 39 residues processed: 179 average time/residue: 0.1705 time to fit residues: 50.5996 Evaluate side-chains 180 residues out of total 2844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 130 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 909 LYS Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1341 ASP Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 443 GLU Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 142 MET Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 231 PHE Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 137 PHE Chi-restraints excluded: chain G residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 300 optimal weight: 4.9990 chunk 233 optimal weight: 0.0870 chunk 312 optimal weight: 5.9990 chunk 240 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.039644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.030003 restraints weight = 190969.163| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.90 r_work: 0.2744 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28778 Z= 0.134 Angle : 0.556 13.049 39267 Z= 0.292 Chirality : 0.041 0.265 4435 Planarity : 0.004 0.066 4796 Dihedral : 17.191 174.213 4749 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.70 % Favored : 97.24 % Rotamer: Outliers : 1.79 % Allowed : 19.34 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.29 (0.15), residues: 3294 helix: 1.91 (0.14), residues: 1342 sheet: 0.02 (0.25), residues: 412 loop : 0.25 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 634 TYR 0.012 0.001 TYR B 631 PHE 0.011 0.001 PHE D 231 TRP 0.007 0.001 TRP G 36 HIS 0.011 0.001 HIS D 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (28778) covalent geometry : angle 0.55564 / 0.29 (39267) hydrogen bonds : bond 0.03692 / 2.42 ( 1320) hydrogen bonds : angle 4.44001 / 3.15 ( 3682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5956.61 seconds wall clock time: 103 minutes 8.82 seconds (6188.82 seconds total)