Starting phenix.real_space_refine on Sun Jun 22 08:38:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t02_40931/06_2025/8t02_40931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t02_40931/06_2025/8t02_40931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t02_40931/06_2025/8t02_40931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t02_40931/06_2025/8t02_40931.map" model { file = "/net/cci-nas-00/data/ceres_data/8t02_40931/06_2025/8t02_40931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t02_40931/06_2025/8t02_40931.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 49 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 15920 2.51 5 N 4509 2.21 5 O 5014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25601 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1705 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1318, 10397 Classifications: {'peptide': 1318} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1262} Chain breaks: 1 Chain: "J" Number of atoms: 10240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10240 Classifications: {'peptide': 1316} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1261} Chain breaks: 3 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "A" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "B" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 460 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14224 SG CYS J 70 97.450 108.353 98.961 1.00183.94 S ATOM 14238 SG CYS J 72 99.675 110.221 101.104 1.00182.54 S ATOM 14346 SG CYS J 85 98.361 112.202 98.326 1.00183.85 S ATOM 14370 SG CYS J 88 99.729 108.318 97.797 1.00184.25 S ATOM 19921 SG CYS J 814 57.298 72.229 58.546 1.00 96.28 S ATOM 20486 SG CYS J 888 60.317 72.044 60.645 1.00 85.91 S ATOM 20537 SG CYS J 895 58.588 71.307 61.359 1.00 82.58 S ATOM 20558 SG CYS J 898 58.473 70.268 61.270 1.00 84.30 S Time building chain proxies: 14.55, per 1000 atoms: 0.57 Number of scatterers: 25601 At special positions: 0 Unit cell: (166.78, 123.74, 164.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 49 15.00 Mg 1 11.99 O 5014 8.00 N 4509 7.00 C 15920 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: 7.15 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5810 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 44 sheets defined 39.3% alpha, 15.4% beta 19 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 9.39 Creating SS restraints... Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 87 Processing helix chain 'G' and resid 154 through 159 removed outlier: 4.024A pdb=" N ARG G 158 " --> pdb=" O PRO G 154 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 154 through 159' Processing helix chain 'G' and resid 212 through 233 removed outlier: 3.867A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 49 removed outlier: 3.660A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 88 removed outlier: 3.540A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 230 removed outlier: 4.051A pdb=" N ALA H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 28 through 39 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.502A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 242 through 246 Processing helix chain 'I' and resid 270 through 280 Processing helix chain 'I' and resid 288 through 294 removed outlier: 3.935A pdb=" N ILE I 292 " --> pdb=" O PRO I 288 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA I 293 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 288 through 294' Processing helix chain 'I' and resid 318 through 329 removed outlier: 4.126A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 354 Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.790A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 393 No H-bonds generated for 'chain 'I' and resid 391 through 393' Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 Processing helix chain 'I' and resid 447 through 449 No H-bonds generated for 'chain 'I' and resid 447 through 449' Processing helix chain 'I' and resid 455 through 480 Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 520 through 527 Processing helix chain 'I' and resid 539 through 543 removed outlier: 3.690A pdb=" N ALA I 543 " --> pdb=" O ARG I 540 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 614 removed outlier: 3.887A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 609 through 614' Processing helix chain 'I' and resid 646 through 650 removed outlier: 3.958A pdb=" N VAL I 650 " --> pdb=" O ARG I 647 " (cutoff:3.500A) Processing helix chain 'I' and resid 662 through 667 removed outlier: 4.200A pdb=" N LEU I 667 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 removed outlier: 3.829A pdb=" N ARG I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 704 through 712 Processing helix chain 'I' and resid 819 through 825 removed outlier: 4.083A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 864 removed outlier: 3.639A pdb=" N LEU I 862 " --> pdb=" O GLY I 858 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS I 864 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 980 Processing helix chain 'I' and resid 985 through 992 removed outlier: 3.627A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 1005 through 1038 removed outlier: 3.909A pdb=" N ASN I1009 " --> pdb=" O GLU I1005 " (cutoff:3.500A) Processing helix chain 'I' and resid 1081 through 1085 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.431A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG I1106 " --> pdb=" O GLY I1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1101 through 1106' Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.567A pdb=" N LEU I1113 " --> pdb=" O ILE I1109 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1151 Processing helix chain 'I' and resid 1165 through 1177 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1243 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.592A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1293 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.775A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 Processing helix chain 'J' and resid 26 through 33 Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'J' and resid 95 through 101 removed outlier: 3.751A pdb=" N ARG J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 129 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 173 Processing helix chain 'J' and resid 181 through 191 Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 210 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 246 through 250 Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.245A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 328 through 332 Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 removed outlier: 3.521A pdb=" N ALA J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 417 removed outlier: 3.889A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 450 through 458 removed outlier: 3.670A pdb=" N CYS J 454 " --> pdb=" O HIS J 450 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.823A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 593 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 636 removed outlier: 3.920A pdb=" N TYR J 631 " --> pdb=" O THR J 627 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 removed outlier: 3.755A pdb=" N MET J 644 " --> pdb=" O ILE J 641 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 670 removed outlier: 4.024A pdb=" N GLU J 652 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 3.810A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 Processing helix chain 'J' and resid 733 through 742 removed outlier: 4.044A pdb=" N GLN J 739 " --> pdb=" O ALA J 735 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU J 740 " --> pdb=" O GLN J 736 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 804 removed outlier: 3.962A pdb=" N LYS J 781 " --> pdb=" O HIS J 777 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY J 782 " --> pdb=" O GLY J 778 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.597A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 884 through 888 Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 removed outlier: 4.307A pdb=" N ILE J 918 " --> pdb=" O ALA J 914 " (cutoff:3.500A) Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1068 through 1073 removed outlier: 3.725A pdb=" N ASP J1073 " --> pdb=" O ALA J1069 " (cutoff:3.500A) Processing helix chain 'J' and resid 1137 through 1147 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1244 removed outlier: 3.962A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1249 through 1261 removed outlier: 4.338A pdb=" N ILE J1253 " --> pdb=" O ASN J1249 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 Processing helix chain 'J' and resid 1308 through 1315 Processing helix chain 'J' and resid 1318 through 1324 removed outlier: 3.661A pdb=" N ALA J1322 " --> pdb=" O SER J1318 " (cutoff:3.500A) Processing helix chain 'J' and resid 1328 through 1339 Processing helix chain 'J' and resid 1347 through 1354 Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 4.089A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG J1371 " --> pdb=" O GLN J1367 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG J1373 " --> pdb=" O ARG J1369 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 33 removed outlier: 4.043A pdb=" N GLY K 33 " --> pdb=" O GLN K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 57 Processing helix chain 'K' and resid 62 through 74 Processing sheet with id=AA1, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.958A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 61 removed outlier: 5.707A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'H' and resid 12 through 18 removed outlier: 5.100A pdb=" N LEU H 13 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLU H 29 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP H 15 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASP H 199 " --> pdb=" O PRO H 30 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG H 182 " --> pdb=" O GLU H 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 101 removed outlier: 6.666A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'H' and resid 108 through 111 removed outlier: 3.591A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.241A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE I 104 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.576A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AB6, first strand: chain 'I' and resid 284 through 285 removed outlier: 5.229A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.753A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 301 through 302 removed outlier: 6.939A pdb=" N TYR I 301 " --> pdb=" O ILE I 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.562A pdb=" N ARG I 731 " --> pdb=" O VAL I 727 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL I 727 " --> pdb=" O ARG I 731 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL I 733 " --> pdb=" O GLN I 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'I' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'I' and resid 817 through 818 removed outlier: 3.695A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA I1067 " --> pdb=" O LEU I1233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 817 through 818 removed outlier: 3.695A pdb=" N LEU I 817 " --> pdb=" O VAL I1097 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ILE I1096 " --> pdb=" O ASN I 799 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG I 801 " --> pdb=" O ILE I1096 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU I1098 " --> pdb=" O ARG I 801 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA I 803 " --> pdb=" O LEU I1098 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 846 through 847 removed outlier: 3.676A pdb=" N THR I 843 " --> pdb=" O GLY I 846 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 882 through 884 removed outlier: 7.137A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD1, first strand: chain 'I' and resid 1244 through 1245 removed outlier: 3.502A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 1244 through 1245 removed outlier: 7.119A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU J 449 " --> pdb=" O VAL J 354 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR J 356 " --> pdb=" O LEU J 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD5, first strand: chain 'J' and resid 34 through 37 removed outlier: 5.239A pdb=" N SER J 34 " --> pdb=" O MET J 102 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS J 104 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY J 36 " --> pdb=" O HIS J 104 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU J 106 " --> pdb=" O GLY J 36 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N LEU J 107 " --> pdb=" O PRO J 243 " (cutoff:3.500A) removed outlier: 10.753A pdb=" N SER J 109 " --> pdb=" O VAL J 241 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL J 241 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 159 through 160 removed outlier: 3.539A pdb=" N VAL J 145 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS J 179 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE J 147 " --> pdb=" O ASP J 177 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP J 177 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 526 through 527 removed outlier: 3.641A pdb=" N ILE J 552 " --> pdb=" O SER J 568 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER J 568 " --> pdb=" O ILE J 552 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AD9, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'J' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.873A pdb=" N GLU J 993 " --> pdb=" O LEU J 984 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU J 984 " --> pdb=" O GLU J 993 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL J1011 " --> pdb=" O GLY J 956 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AE4, first strand: chain 'J' and resid 1001 through 1002 Processing sheet with id=AE5, first strand: chain 'J' and resid 1098 through 1100 removed outlier: 4.530A pdb=" N VAL J1113 " --> pdb=" O VAL J1035 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1046 through 1049 removed outlier: 3.825A pdb=" N GLN J1049 " --> pdb=" O SER J1058 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1188 through 1190 removed outlier: 3.725A pdb=" N VAL J1204 " --> pdb=" O GLY J1161 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 6.541A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2841 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 38 hydrogen bonds 76 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 12.92 Time building geometry restraints manager: 8.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8504 1.34 - 1.46: 3819 1.46 - 1.58: 13479 1.58 - 1.70: 95 1.70 - 1.82: 184 Bond restraints: 26081 Sorted by residual: bond pdb=" C3' DA A 13 " pdb=" O3' DA A 13 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" C3' DT B 118 " pdb=" O3' DT B 118 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.05e+00 bond pdb=" N GLU G 7 " pdb=" CA GLU G 7 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.90e-02 2.77e+03 1.98e+00 bond pdb=" C LYS J 40 " pdb=" N PRO J 41 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.92e+00 bond pdb=" C1' DT B 105 " pdb=" N1 DT B 105 " ideal model delta sigma weight residual 1.490 1.527 -0.037 3.00e-02 1.11e+03 1.52e+00 ... (remaining 26076 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 34794 1.95 - 3.89: 565 3.89 - 5.84: 64 5.84 - 7.78: 7 7.78 - 9.73: 2 Bond angle restraints: 35432 Sorted by residual: angle pdb=" CB MET I1315 " pdb=" CG MET I1315 " pdb=" SD MET I1315 " ideal model delta sigma weight residual 112.70 122.43 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C3' DA A 13 " pdb=" O3' DA A 13 " pdb=" P DA A 14 " ideal model delta sigma weight residual 120.20 124.54 -4.34 1.50e+00 4.44e-01 8.36e+00 angle pdb=" N ASP J1184 " pdb=" CA ASP J1184 " pdb=" C ASP J1184 " ideal model delta sigma weight residual 109.81 115.78 -5.97 2.21e+00 2.05e-01 7.31e+00 angle pdb=" CA MET J1370 " pdb=" CB MET J1370 " pdb=" CG MET J1370 " ideal model delta sigma weight residual 114.10 119.40 -5.30 2.00e+00 2.50e-01 7.01e+00 angle pdb=" CB MET I1170 " pdb=" CG MET I1170 " pdb=" SD MET I1170 " ideal model delta sigma weight residual 112.70 120.55 -7.85 3.00e+00 1.11e-01 6.85e+00 ... (remaining 35427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.02: 15339 34.02 - 68.04: 597 68.04 - 102.06: 32 102.06 - 136.08: 0 136.08 - 170.10: 3 Dihedral angle restraints: 15971 sinusoidal: 6941 harmonic: 9030 Sorted by residual: dihedral pdb=" CA ASP J1184 " pdb=" C ASP J1184 " pdb=" N PRO J1185 " pdb=" CA PRO J1185 " ideal model delta harmonic sigma weight residual -180.00 -149.31 -30.69 0 5.00e+00 4.00e-02 3.77e+01 dihedral pdb=" CA ASN I 519 " pdb=" C ASN I 519 " pdb=" N PRO I 520 " pdb=" CA PRO I 520 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.41e+01 dihedral pdb=" CA SER J 753 " pdb=" C SER J 753 " pdb=" N ILE J 754 " pdb=" CA ILE J 754 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 15968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2547 0.030 - 0.060: 977 0.060 - 0.090: 284 0.090 - 0.121: 204 0.121 - 0.151: 39 Chirality restraints: 4051 Sorted by residual: chirality pdb=" CA VAL G 146 " pdb=" N VAL G 146 " pdb=" C VAL G 146 " pdb=" CB VAL G 146 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE I 177 " pdb=" N ILE I 177 " pdb=" C ILE I 177 " pdb=" CB ILE I 177 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CA PRO J 750 " pdb=" N PRO J 750 " pdb=" C PRO J 750 " pdb=" CB PRO J 750 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.39e-01 ... (remaining 4048 not shown) Planarity restraints: 4467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " -0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO J 359 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 697 " -0.042 5.00e-02 4.00e+02 6.37e-02 6.50e+00 pdb=" N PRO I 698 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO I 698 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 698 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 850 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO J 851 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO J 851 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 851 " 0.033 5.00e-02 4.00e+02 ... (remaining 4464 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 324 2.56 - 3.15: 22503 3.15 - 3.73: 40195 3.73 - 4.32: 53892 4.32 - 4.90: 88714 Nonbonded interactions: 205628 Sorted by model distance: nonbonded pdb=" OE1 GLU I 562 " pdb=" OG SER I 662 " model vdw 1.981 3.040 nonbonded pdb=" OG1 THR G 22 " pdb=" O THR G 207 " model vdw 1.991 3.040 nonbonded pdb=" OG SER I 421 " pdb=" OD1 ASP I 423 " model vdw 2.014 3.040 nonbonded pdb=" OG1 THR I 6 " pdb=" OD2 ASP I 781 " model vdw 2.018 3.040 nonbonded pdb=" OH TYR J 360 " pdb=" OE1 GLN J 448 " model vdw 2.052 3.040 ... (remaining 205623 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 'G' and (resid 7 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 149 or (resid 150 and (name N or \ name CA or name C or name O or name CB )) or resid 151 through 158 or resid 170 \ through 232)) selection = (chain 'H' and (resid 7 through 190 or (resid 191 through 192 and (name N or nam \ e CA or name C or name O or name CB )) or resid 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.260 Process input model: 72.380 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 26089 Z= 0.158 Angle : 0.886 83.021 35444 Z= 0.347 Chirality : 0.041 0.151 4051 Planarity : 0.004 0.070 4467 Dihedral : 16.694 170.103 10161 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.45 % Rotamer: Outliers : 1.53 % Allowed : 16.25 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 3124 helix: 0.80 (0.16), residues: 1065 sheet: -1.28 (0.25), residues: 362 loop : -1.67 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 236 HIS 0.005 0.001 HIS J1366 PHE 0.017 0.001 PHE I 230 TYR 0.024 0.001 TYR I1229 ARG 0.014 0.000 ARG I1033 Details of bonding type rmsd hydrogen bonds : bond 0.15933 ( 1046) hydrogen bonds : angle 6.49414 ( 2917) metal coordination : bond 0.04809 ( 8) metal coordination : angle 34.94997 ( 12) covalent geometry : bond 0.00350 (26081) covalent geometry : angle 0.60965 (35432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 746 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 10 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7319 (mppt) REVERT: G 58 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6612 (mt-10) REVERT: G 199 ASP cc_start: 0.7504 (m-30) cc_final: 0.7125 (m-30) REVERT: H 128 HIS cc_start: 0.8333 (t-90) cc_final: 0.7669 (t-90) REVERT: I 14 ASP cc_start: 0.8078 (t0) cc_final: 0.7801 (t0) REVERT: I 37 LYS cc_start: 0.8558 (ttpt) cc_final: 0.8007 (tptt) REVERT: I 211 ARG cc_start: 0.8428 (ttt180) cc_final: 0.8154 (ptt180) REVERT: I 218 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8615 (pp20) REVERT: I 359 ARG cc_start: 0.7577 (ttt-90) cc_final: 0.6759 (ttt-90) REVERT: I 360 LEU cc_start: 0.8841 (tt) cc_final: 0.8638 (tt) REVERT: I 361 SER cc_start: 0.9110 (m) cc_final: 0.8875 (p) REVERT: I 731 ARG cc_start: 0.7986 (ptp90) cc_final: 0.7715 (ptp90) REVERT: I 1089 GLU cc_start: 0.8014 (tp30) cc_final: 0.7606 (tp30) REVERT: I 1090 ASN cc_start: 0.8692 (t0) cc_final: 0.8437 (t0) REVERT: I 1240 ASP cc_start: 0.8568 (p0) cc_final: 0.7987 (t0) REVERT: I 1281 TYR cc_start: 0.8339 (m-80) cc_final: 0.7861 (m-10) REVERT: J 425 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6801 (mtp-110) REVERT: J 462 ASP cc_start: 0.8178 (p0) cc_final: 0.7743 (p0) REVERT: J 553 THR cc_start: 0.8763 (m) cc_final: 0.8305 (p) REVERT: J 568 SER cc_start: 0.8329 (m) cc_final: 0.7563 (m) REVERT: J 569 LEU cc_start: 0.8794 (tp) cc_final: 0.8437 (tp) REVERT: J 614 LEU cc_start: 0.8876 (tp) cc_final: 0.8518 (tt) REVERT: J 1040 MET cc_start: 0.3368 (mtt) cc_final: 0.0603 (ppp) REVERT: J 1280 VAL cc_start: 0.6943 (m) cc_final: 0.6144 (m) REVERT: K 61 ASN cc_start: 0.8216 (m-40) cc_final: 0.7825 (t0) outliers start: 41 outliers final: 25 residues processed: 769 average time/residue: 0.4344 time to fit residues: 498.8781 Evaluate side-chains 561 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 536 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 530 ILE Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 1042 LEU Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain J residue 341 ASN Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 490 ILE Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 833 GLU Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1305 ASP Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1334 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 30.0000 chunk 239 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 127 optimal weight: 20.0000 chunk 247 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 286 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN G 186 ASN I 120 GLN I 133 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 339 ASN I 490 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 952 GLN I1146 GLN I1220 GLN J 157 GLN J 465 GLN J 488 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1010 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1366 HIS K 7 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.206290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139516 restraints weight = 44513.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139787 restraints weight = 25355.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140743 restraints weight = 17172.745| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 26089 Z= 0.184 Angle : 0.737 18.527 35444 Z= 0.366 Chirality : 0.045 0.227 4051 Planarity : 0.005 0.082 4467 Dihedral : 14.523 175.906 4068 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.11 % Favored : 93.85 % Rotamer: Outliers : 3.85 % Allowed : 18.71 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 3124 helix: 0.81 (0.16), residues: 1102 sheet: -1.00 (0.24), residues: 394 loop : -1.65 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 997 HIS 0.004 0.001 HIS G 23 PHE 0.019 0.001 PHE I 80 TYR 0.020 0.002 TYR J 772 ARG 0.009 0.001 ARG G 12 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 1046) hydrogen bonds : angle 5.34084 ( 2917) metal coordination : bond 0.01349 ( 8) metal coordination : angle 10.95039 ( 12) covalent geometry : bond 0.00428 (26081) covalent geometry : angle 0.70937 (35432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 580 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 51 MET cc_start: 0.8905 (mmm) cc_final: 0.8648 (mmm) REVERT: G 58 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7113 (mt-10) REVERT: G 71 LYS cc_start: 0.8492 (tptt) cc_final: 0.8101 (tptm) REVERT: G 125 LYS cc_start: 0.8641 (tttt) cc_final: 0.8169 (tttm) REVERT: G 199 ASP cc_start: 0.7585 (m-30) cc_final: 0.7055 (m-30) REVERT: I 8 LYS cc_start: 0.9070 (mttt) cc_final: 0.8567 (mttm) REVERT: I 37 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8093 (tptm) REVERT: I 97 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7065 (mmm-85) REVERT: I 121 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8261 (tm-30) REVERT: I 130 MET cc_start: 0.8321 (ttm) cc_final: 0.8012 (ttm) REVERT: I 151 ARG cc_start: 0.8135 (ttt-90) cc_final: 0.7843 (mtp85) REVERT: I 211 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8121 (ptt180) REVERT: I 218 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8737 (pp20) REVERT: I 369 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8503 (ppp) REVERT: I 614 TYR cc_start: 0.7928 (m-80) cc_final: 0.7710 (m-80) REVERT: I 653 MET cc_start: 0.8094 (tpp) cc_final: 0.7723 (tpt) REVERT: I 731 ARG cc_start: 0.7883 (ptp90) cc_final: 0.7537 (ptp90) REVERT: I 932 GLN cc_start: 0.6236 (tp40) cc_final: 0.5950 (tp40) REVERT: I 933 VAL cc_start: 0.7986 (t) cc_final: 0.7536 (t) REVERT: I 952 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8266 (tm-30) REVERT: I 958 LYS cc_start: 0.9183 (tmtt) cc_final: 0.8756 (tptp) REVERT: I 1089 GLU cc_start: 0.8213 (tp30) cc_final: 0.7840 (tp30) REVERT: I 1166 ASP cc_start: 0.8588 (m-30) cc_final: 0.7872 (t0) REVERT: I 1170 MET cc_start: 0.8209 (mmt) cc_final: 0.7776 (mmt) REVERT: I 1174 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8162 (tp30) REVERT: I 1229 TYR cc_start: 0.8545 (m-10) cc_final: 0.8237 (m-10) REVERT: I 1240 ASP cc_start: 0.8673 (p0) cc_final: 0.7957 (t70) REVERT: I 1281 TYR cc_start: 0.8784 (m-80) cc_final: 0.8398 (m-10) REVERT: I 1290 MET cc_start: 0.8465 (tpp) cc_final: 0.7952 (tpp) REVERT: I 1304 MET cc_start: 0.7784 (ttm) cc_final: 0.7490 (ttm) REVERT: J 403 ARG cc_start: 0.8289 (mmp80) cc_final: 0.8070 (mmp80) REVERT: J 449 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7488 (tp) REVERT: J 521 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: J 553 THR cc_start: 0.8977 (m) cc_final: 0.8571 (p) REVERT: J 891 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7362 (t0) REVERT: J 1003 LEU cc_start: 0.8063 (tp) cc_final: 0.7822 (tp) REVERT: J 1040 MET cc_start: 0.3771 (mtt) cc_final: 0.0881 (ppp) REVERT: J 1189 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7110 (tmm) REVERT: J 1224 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7930 (tpp80) REVERT: K 63 ILE cc_start: 0.8542 (tp) cc_final: 0.8320 (pt) outliers start: 103 outliers final: 51 residues processed: 643 average time/residue: 0.4059 time to fit residues: 395.0199 Evaluate side-chains 550 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 492 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 368 LEU Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 521 LYS Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 1027 VAL Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1224 ARG Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 120 optimal weight: 7.9990 chunk 221 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 265 optimal weight: 30.0000 chunk 212 optimal weight: 1.9990 chunk 204 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 275 optimal weight: 50.0000 chunk 49 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN G 186 ASN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1090 ASN J 720 ASN ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 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 = 0.4531 r_free = 0.4531 target = 0.205603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140469 restraints weight = 44240.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.139492 restraints weight = 25625.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.139877 restraints weight = 18307.330| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26089 Z= 0.182 Angle : 0.704 13.750 35444 Z= 0.354 Chirality : 0.044 0.213 4051 Planarity : 0.006 0.116 4467 Dihedral : 14.455 179.782 4040 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 3.77 % Allowed : 19.05 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3124 helix: 0.80 (0.16), residues: 1101 sheet: -0.84 (0.25), residues: 385 loop : -1.60 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 997 HIS 0.004 0.001 HIS J 104 PHE 0.023 0.001 PHE I 80 TYR 0.025 0.002 TYR H 177 ARG 0.010 0.001 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1046) hydrogen bonds : angle 5.18483 ( 2917) metal coordination : bond 0.01264 ( 8) metal coordination : angle 6.62040 ( 12) covalent geometry : bond 0.00422 (26081) covalent geometry : angle 0.69394 (35432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 538 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: G 10 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7073 (mmtm) REVERT: G 51 MET cc_start: 0.8897 (mmm) cc_final: 0.8595 (mmm) REVERT: G 125 LYS cc_start: 0.8620 (tttt) cc_final: 0.8156 (tttm) REVERT: G 145 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8299 (tptp) REVERT: G 181 GLU cc_start: 0.7171 (mp0) cc_final: 0.6934 (mp0) REVERT: G 186 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8295 (p0) REVERT: G 199 ASP cc_start: 0.7257 (m-30) cc_final: 0.6954 (m-30) REVERT: G 206 GLU cc_start: 0.7050 (tp30) cc_final: 0.6622 (tp30) REVERT: H 132 HIS cc_start: 0.8092 (m-70) cc_final: 0.7644 (m-70) REVERT: I 37 LYS cc_start: 0.8555 (ttpt) cc_final: 0.7955 (tttm) REVERT: I 97 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7167 (mmm-85) REVERT: I 121 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8284 (tm-30) REVERT: I 202 ARG cc_start: 0.8337 (ptt180) cc_final: 0.7993 (ptt180) REVERT: I 211 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8216 (ptt180) REVERT: I 218 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8761 (pp20) REVERT: I 369 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8511 (tmm) REVERT: I 384 LEU cc_start: 0.8713 (tt) cc_final: 0.8397 (mt) REVERT: I 431 LYS cc_start: 0.8683 (tppt) cc_final: 0.8467 (tppt) REVERT: I 614 TYR cc_start: 0.7863 (m-80) cc_final: 0.7632 (m-80) REVERT: I 653 MET cc_start: 0.8071 (tpp) cc_final: 0.7806 (tpt) REVERT: I 731 ARG cc_start: 0.8017 (ptp90) cc_final: 0.7530 (ptp90) REVERT: I 820 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: I 932 GLN cc_start: 0.6485 (tp40) cc_final: 0.6146 (tp40) REVERT: I 933 VAL cc_start: 0.8030 (t) cc_final: 0.7427 (t) REVERT: I 951 MET cc_start: 0.8992 (tmm) cc_final: 0.8647 (ppp) REVERT: I 958 LYS cc_start: 0.9227 (tmtt) cc_final: 0.8664 (tptp) REVERT: I 1089 GLU cc_start: 0.8241 (tp30) cc_final: 0.7932 (tp30) REVERT: I 1166 ASP cc_start: 0.8673 (m-30) cc_final: 0.7839 (t0) REVERT: I 1170 MET cc_start: 0.8328 (mmt) cc_final: 0.7861 (mmt) REVERT: I 1174 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7948 (tp30) REVERT: I 1180 MET cc_start: 0.7564 (ttp) cc_final: 0.7302 (ttp) REVERT: I 1194 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: I 1230 MET cc_start: 0.8654 (ttp) cc_final: 0.8225 (ttt) REVERT: I 1240 ASP cc_start: 0.8721 (p0) cc_final: 0.8136 (t70) REVERT: I 1241 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8565 (t0) REVERT: I 1281 TYR cc_start: 0.8882 (m-80) cc_final: 0.8566 (m-10) REVERT: I 1290 MET cc_start: 0.8692 (tpp) cc_final: 0.7831 (tpp) REVERT: I 1304 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7431 (ttm) REVERT: J 123 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7055 (mmp80) REVERT: J 400 MET cc_start: 0.7891 (mmm) cc_final: 0.7591 (mmm) REVERT: J 417 ARG cc_start: 0.8121 (tpt170) cc_final: 0.7733 (mmm-85) REVERT: J 449 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7937 (mt) REVERT: J 553 THR cc_start: 0.8940 (m) cc_final: 0.8529 (p) REVERT: J 614 LEU cc_start: 0.8787 (tp) cc_final: 0.8540 (tt) REVERT: J 891 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7439 (t0) REVERT: J 1003 LEU cc_start: 0.7977 (tp) cc_final: 0.7701 (tp) REVERT: J 1040 MET cc_start: 0.4531 (mtt) cc_final: 0.1664 (ppp) REVERT: J 1156 LEU cc_start: 0.9623 (tp) cc_final: 0.9390 (tp) REVERT: J 1189 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7131 (tmm) REVERT: K 26 ARG cc_start: 0.8826 (tpm170) cc_final: 0.8226 (tpm170) REVERT: K 29 GLN cc_start: 0.9017 (mt0) cc_final: 0.8701 (mp10) REVERT: K 52 ARG cc_start: 0.8794 (mtp180) cc_final: 0.8318 (ptm160) REVERT: K 61 ASN cc_start: 0.8170 (t0) cc_final: 0.7642 (t0) outliers start: 101 outliers final: 64 residues processed: 596 average time/residue: 0.4128 time to fit residues: 375.9593 Evaluate side-chains 560 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 486 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 600 THR Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 820 GLU Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1304 MET Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 30.0000 chunk 158 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 276 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 HIS I1090 ASN J 430 HIS ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.198587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126593 restraints weight = 44930.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125978 restraints weight = 28725.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126144 restraints weight = 22970.943| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.090 26089 Z= 0.402 Angle : 0.860 15.757 35444 Z= 0.439 Chirality : 0.049 0.283 4051 Planarity : 0.007 0.097 4467 Dihedral : 14.635 178.428 4036 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.59 % Favored : 92.38 % Rotamer: Outliers : 6.09 % Allowed : 19.50 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3124 helix: 0.40 (0.15), residues: 1108 sheet: -1.04 (0.24), residues: 421 loop : -1.72 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 183 HIS 0.010 0.002 HIS I1023 PHE 0.037 0.003 PHE I 506 TYR 0.029 0.003 TYR H 177 ARG 0.008 0.001 ARG J 799 Details of bonding type rmsd hydrogen bonds : bond 0.05129 ( 1046) hydrogen bonds : angle 5.60150 ( 2917) metal coordination : bond 0.02094 ( 8) metal coordination : angle 6.58276 ( 12) covalent geometry : bond 0.00918 (26081) covalent geometry : angle 0.85167 (35432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 497 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7202 (mmtm) REVERT: G 35 PHE cc_start: 0.8592 (m-80) cc_final: 0.7979 (m-80) REVERT: G 125 LYS cc_start: 0.8675 (tttt) cc_final: 0.8032 (tttm) REVERT: G 181 GLU cc_start: 0.7502 (mp0) cc_final: 0.6935 (mp0) REVERT: G 206 GLU cc_start: 0.7072 (tp30) cc_final: 0.6515 (tp30) REVERT: H 177 TYR cc_start: 0.8394 (m-10) cc_final: 0.8177 (m-10) REVERT: I 8 LYS cc_start: 0.9192 (mttt) cc_final: 0.8571 (mttm) REVERT: I 37 LYS cc_start: 0.8728 (ttpt) cc_final: 0.8131 (tttm) REVERT: I 97 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7021 (mmm-85) REVERT: I 121 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8249 (tm-30) REVERT: I 151 ARG cc_start: 0.8175 (ttt-90) cc_final: 0.7909 (mtp85) REVERT: I 211 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8382 (ptt180) REVERT: I 218 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8781 (pp20) REVERT: I 346 TYR cc_start: 0.7862 (m-80) cc_final: 0.7620 (m-80) REVERT: I 363 LEU cc_start: 0.9423 (mt) cc_final: 0.9138 (tp) REVERT: I 431 LYS cc_start: 0.8804 (tppt) cc_final: 0.8547 (tppt) REVERT: I 477 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8852 (mt-10) REVERT: I 565 GLU cc_start: 0.8196 (mp0) cc_final: 0.7944 (mp0) REVERT: I 614 TYR cc_start: 0.7982 (m-80) cc_final: 0.7754 (m-80) REVERT: I 731 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7648 (ptp90) REVERT: I 932 GLN cc_start: 0.6875 (tp40) cc_final: 0.6440 (tp40) REVERT: I 958 LYS cc_start: 0.9354 (tmtt) cc_final: 0.8924 (tptp) REVERT: I 1034 ARG cc_start: 0.9442 (tpt90) cc_final: 0.9014 (tpt90) REVERT: I 1089 GLU cc_start: 0.8384 (tp30) cc_final: 0.8091 (tp30) REVERT: I 1166 ASP cc_start: 0.8600 (m-30) cc_final: 0.7718 (t0) REVERT: I 1170 MET cc_start: 0.8398 (mmt) cc_final: 0.7954 (mmt) REVERT: I 1174 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8037 (tp30) REVERT: I 1194 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: I 1230 MET cc_start: 0.8940 (ttp) cc_final: 0.8636 (ttt) REVERT: I 1240 ASP cc_start: 0.8798 (p0) cc_final: 0.8410 (t70) REVERT: I 1246 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7880 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8968 (m-80) cc_final: 0.8421 (m-10) REVERT: J 37 GLU cc_start: 0.7977 (tp30) cc_final: 0.7637 (tp30) REVERT: J 123 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7315 (mmp80) REVERT: J 198 CYS cc_start: 0.8825 (m) cc_final: 0.8233 (p) REVERT: J 330 MET cc_start: 0.8028 (tpp) cc_final: 0.7528 (tpp) REVERT: J 341 ASN cc_start: 0.8588 (m110) cc_final: 0.7606 (t0) REVERT: J 417 ARG cc_start: 0.8427 (tpt170) cc_final: 0.7934 (mmm160) REVERT: J 449 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7636 (tp) REVERT: J 844 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8171 (t) REVERT: J 891 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7631 (t0) REVERT: J 1003 LEU cc_start: 0.8147 (tp) cc_final: 0.7780 (tp) REVERT: J 1040 MET cc_start: 0.4527 (mtt) cc_final: 0.1809 (ppp) REVERT: J 1156 LEU cc_start: 0.9700 (tp) cc_final: 0.9440 (tp) REVERT: J 1189 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.6783 (tmm) REVERT: K 52 ARG cc_start: 0.9012 (mtp180) cc_final: 0.8370 (ptm160) REVERT: K 61 ASN cc_start: 0.8334 (t0) cc_final: 0.7967 (t0) outliers start: 163 outliers final: 118 residues processed: 607 average time/residue: 0.4017 time to fit residues: 376.0981 Evaluate side-chains 590 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 463 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 479 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 651 ASP Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 715 THR Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 785 ASP Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 830 THR Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1088 ASP Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 507 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 867 GLN Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 892 PHE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1220 ILE Chi-restraints excluded: chain J residue 1233 ILE Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 21 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 32 optimal weight: 50.0000 chunk 181 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 179 optimal weight: 50.0000 chunk 201 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 ASN ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN I 760 ASN ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 HIS ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 777 HIS ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.201603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127339 restraints weight = 44539.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.132123 restraints weight = 25466.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.132679 restraints weight = 16880.385| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26089 Z= 0.236 Angle : 0.731 12.989 35444 Z= 0.371 Chirality : 0.045 0.235 4051 Planarity : 0.006 0.068 4467 Dihedral : 14.568 177.500 4036 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 5.30 % Allowed : 21.44 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 3124 helix: 0.60 (0.15), residues: 1109 sheet: -1.00 (0.25), residues: 408 loop : -1.64 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 868 HIS 0.004 0.001 HIS I 447 PHE 0.020 0.002 PHE I 506 TYR 0.026 0.002 TYR J 772 ARG 0.009 0.001 ARG H 219 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 1046) hydrogen bonds : angle 5.26587 ( 2917) metal coordination : bond 0.01112 ( 8) metal coordination : angle 4.28223 ( 12) covalent geometry : bond 0.00548 (26081) covalent geometry : angle 0.72710 (35432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 505 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7484 (mmtm) REVERT: G 51 MET cc_start: 0.8899 (mmm) cc_final: 0.8655 (mmm) REVERT: G 71 LYS cc_start: 0.8629 (tptt) cc_final: 0.8279 (tptm) REVERT: G 125 LYS cc_start: 0.8673 (tttt) cc_final: 0.8071 (tttm) REVERT: G 181 GLU cc_start: 0.7355 (mp0) cc_final: 0.6822 (mp0) REVERT: G 206 GLU cc_start: 0.7202 (tp30) cc_final: 0.6575 (tp30) REVERT: H 185 TYR cc_start: 0.8841 (p90) cc_final: 0.8494 (p90) REVERT: H 219 ARG cc_start: 0.9023 (mmm-85) cc_final: 0.8628 (mmm-85) REVERT: I 37 LYS cc_start: 0.8711 (ttpt) cc_final: 0.7981 (tttm) REVERT: I 97 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.7028 (mmm-85) REVERT: I 121 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8351 (tm-30) REVERT: I 211 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8427 (ttp-170) REVERT: I 218 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8680 (pp20) REVERT: I 316 GLU cc_start: 0.9257 (mp0) cc_final: 0.8872 (tp30) REVERT: I 429 MET cc_start: 0.8309 (mmp) cc_final: 0.8074 (mmt) REVERT: I 431 LYS cc_start: 0.8736 (tppt) cc_final: 0.8439 (tppt) REVERT: I 477 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.8812 (mt-10) REVERT: I 614 TYR cc_start: 0.7886 (m-80) cc_final: 0.7655 (m-80) REVERT: I 731 ARG cc_start: 0.8140 (ptp90) cc_final: 0.7581 (ptp90) REVERT: I 865 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.7824 (mt) REVERT: I 958 LYS cc_start: 0.9355 (tmtt) cc_final: 0.8887 (tptp) REVERT: I 1089 GLU cc_start: 0.8228 (tp30) cc_final: 0.7900 (tp30) REVERT: I 1166 ASP cc_start: 0.8644 (m-30) cc_final: 0.7745 (t0) REVERT: I 1170 MET cc_start: 0.8418 (mmt) cc_final: 0.7971 (mmt) REVERT: I 1174 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8150 (tp30) REVERT: I 1194 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: I 1230 MET cc_start: 0.8880 (ttp) cc_final: 0.8531 (ttt) REVERT: I 1240 ASP cc_start: 0.8783 (p0) cc_final: 0.8368 (t0) REVERT: I 1243 MET cc_start: 0.8790 (ttp) cc_final: 0.8550 (tmm) REVERT: I 1246 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7995 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8884 (m-80) cc_final: 0.8467 (m-10) REVERT: I 1290 MET cc_start: 0.8932 (tpp) cc_final: 0.8723 (tpp) REVERT: I 1327 LEU cc_start: 0.7884 (tt) cc_final: 0.7587 (pp) REVERT: J 31 ARG cc_start: 0.9441 (mtp85) cc_final: 0.8821 (mmm-85) REVERT: J 37 GLU cc_start: 0.8032 (tp30) cc_final: 0.7724 (tp30) REVERT: J 102 MET cc_start: 0.7567 (tpp) cc_final: 0.7364 (tpp) REVERT: J 123 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7378 (mmp80) REVERT: J 342 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7154 (mt) REVERT: J 417 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7797 (mmm160) REVERT: J 425 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6989 (mtp-110) REVERT: J 449 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7890 (mt) REVERT: J 604 MET cc_start: 0.8431 (ttt) cc_final: 0.8199 (ttt) REVERT: J 739 GLN cc_start: 0.8238 (pt0) cc_final: 0.8036 (pt0) REVERT: J 770 LEU cc_start: 0.8573 (mt) cc_final: 0.8363 (mt) REVERT: J 835 LEU cc_start: 0.7668 (tt) cc_final: 0.7442 (tp) REVERT: J 844 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8131 (t) REVERT: J 891 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7565 (t0) REVERT: J 930 LEU cc_start: 0.8293 (mt) cc_final: 0.8081 (mp) REVERT: J 1003 LEU cc_start: 0.8219 (tp) cc_final: 0.7914 (tp) REVERT: J 1040 MET cc_start: 0.4641 (mtt) cc_final: 0.1970 (ppp) REVERT: J 1156 LEU cc_start: 0.9680 (tp) cc_final: 0.9428 (tp) REVERT: J 1189 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7263 (tmm) REVERT: J 1281 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8056 (tm-30) REVERT: J 1284 ARG cc_start: 0.8914 (mmm160) cc_final: 0.8424 (mmm160) REVERT: K 29 GLN cc_start: 0.9141 (mt0) cc_final: 0.8148 (tm-30) REVERT: K 52 ARG cc_start: 0.8802 (mtp180) cc_final: 0.8187 (ptm160) REVERT: K 61 ASN cc_start: 0.8348 (t0) cc_final: 0.8010 (t0) REVERT: K 70 GLN cc_start: 0.9379 (tm-30) cc_final: 0.8759 (pp30) outliers start: 142 outliers final: 94 residues processed: 598 average time/residue: 0.3994 time to fit residues: 365.1898 Evaluate side-chains 569 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 463 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 398 SER Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 477 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 763 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 830 ASP Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 15 ASN Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 214 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 760 ASN ** I 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1195 GLN ** J1249 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 = 0.4505 r_free = 0.4505 target = 0.202885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128002 restraints weight = 44434.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134019 restraints weight = 23597.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134119 restraints weight = 15857.720| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26089 Z= 0.197 Angle : 0.710 15.334 35444 Z= 0.359 Chirality : 0.044 0.228 4051 Planarity : 0.005 0.066 4467 Dihedral : 14.468 176.143 4035 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.59 % Favored : 93.37 % Rotamer: Outliers : 4.97 % Allowed : 22.60 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3124 helix: 0.70 (0.15), residues: 1101 sheet: -1.04 (0.24), residues: 419 loop : -1.58 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I1276 HIS 0.006 0.001 HIS J 777 PHE 0.022 0.002 PHE J1319 TYR 0.034 0.002 TYR H 177 ARG 0.012 0.001 ARG J 337 Details of bonding type rmsd hydrogen bonds : bond 0.04204 ( 1046) hydrogen bonds : angle 5.12365 ( 2917) metal coordination : bond 0.00877 ( 8) metal coordination : angle 3.25250 ( 12) covalent geometry : bond 0.00460 (26081) covalent geometry : angle 0.70789 (35432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 494 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 10 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7681 (mmtm) REVERT: G 51 MET cc_start: 0.8936 (mmm) cc_final: 0.8660 (mmm) REVERT: G 71 LYS cc_start: 0.8602 (tptt) cc_final: 0.8242 (tptm) REVERT: G 181 GLU cc_start: 0.7301 (mp0) cc_final: 0.6748 (mp0) REVERT: G 206 GLU cc_start: 0.7225 (tp30) cc_final: 0.6576 (tp30) REVERT: H 18 GLN cc_start: 0.8916 (pm20) cc_final: 0.8612 (mp10) REVERT: H 127 GLN cc_start: 0.9251 (pm20) cc_final: 0.9051 (pm20) REVERT: H 147 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8299 (tm-30) REVERT: H 219 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8625 (mmm-85) REVERT: I 37 LYS cc_start: 0.8668 (ttpt) cc_final: 0.7828 (tttm) REVERT: I 97 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.7258 (mmm-85) REVERT: I 121 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8396 (tm-30) REVERT: I 122 VAL cc_start: 0.8646 (p) cc_final: 0.8316 (t) REVERT: I 211 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8490 (ptt180) REVERT: I 218 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8740 (mt-10) REVERT: I 429 MET cc_start: 0.8258 (mmp) cc_final: 0.8038 (mmt) REVERT: I 431 LYS cc_start: 0.8729 (tppt) cc_final: 0.8415 (tppt) REVERT: I 479 LEU cc_start: 0.9318 (tp) cc_final: 0.9107 (pp) REVERT: I 654 ASP cc_start: 0.7283 (m-30) cc_final: 0.6960 (m-30) REVERT: I 731 ARG cc_start: 0.8122 (ptp90) cc_final: 0.7565 (ptp90) REVERT: I 865 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.7845 (mt) REVERT: I 951 MET cc_start: 0.9048 (tmm) cc_final: 0.8614 (ppp) REVERT: I 958 LYS cc_start: 0.9361 (tmtt) cc_final: 0.8947 (tptp) REVERT: I 1032 LYS cc_start: 0.9497 (mmtm) cc_final: 0.9296 (mmtm) REVERT: I 1089 GLU cc_start: 0.8286 (tp30) cc_final: 0.7946 (tp30) REVERT: I 1166 ASP cc_start: 0.8481 (m-30) cc_final: 0.7734 (t0) REVERT: I 1170 MET cc_start: 0.8310 (mmt) cc_final: 0.7906 (mmt) REVERT: I 1174 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7940 (tp30) REVERT: I 1194 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: I 1230 MET cc_start: 0.8932 (ttp) cc_final: 0.8562 (ttt) REVERT: I 1240 ASP cc_start: 0.8703 (p0) cc_final: 0.8331 (t0) REVERT: I 1243 MET cc_start: 0.8780 (ttp) cc_final: 0.8555 (tmm) REVERT: I 1246 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7719 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8861 (m-80) cc_final: 0.8460 (m-10) REVERT: I 1327 LEU cc_start: 0.7906 (tt) cc_final: 0.7622 (pp) REVERT: I 1332 SER cc_start: 0.7226 (OUTLIER) cc_final: 0.6913 (p) REVERT: J 37 GLU cc_start: 0.8053 (tp30) cc_final: 0.7799 (tp30) REVERT: J 123 ARG cc_start: 0.7801 (mmm160) cc_final: 0.7243 (mmp80) REVERT: J 341 ASN cc_start: 0.8164 (m110) cc_final: 0.7296 (m-40) REVERT: J 342 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7117 (mt) REVERT: J 417 ARG cc_start: 0.8224 (tpt170) cc_final: 0.7582 (mmm160) REVERT: J 449 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7170 (tp) REVERT: J 646 ILE cc_start: 0.8425 (mm) cc_final: 0.7663 (tp) REVERT: J 686 TRP cc_start: 0.7268 (m100) cc_final: 0.6986 (m100) REVERT: J 739 GLN cc_start: 0.8198 (pt0) cc_final: 0.7986 (pt0) REVERT: J 770 LEU cc_start: 0.8521 (mt) cc_final: 0.8308 (mt) REVERT: J 844 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8055 (t) REVERT: J 891 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7556 (t0) REVERT: J 1003 LEU cc_start: 0.8245 (tp) cc_final: 0.7939 (tp) REVERT: J 1040 MET cc_start: 0.4994 (mtt) cc_final: 0.2578 (ppp) REVERT: J 1156 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9456 (tp) REVERT: J 1189 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7108 (tmm) REVERT: J 1281 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7959 (tm-30) REVERT: J 1284 ARG cc_start: 0.8960 (mmm160) cc_final: 0.8433 (mmm160) REVERT: K 29 GLN cc_start: 0.9104 (mt0) cc_final: 0.8098 (tm-30) outliers start: 133 outliers final: 100 residues processed: 581 average time/residue: 0.4164 time to fit residues: 374.0268 Evaluate side-chains 579 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 467 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 558 VAL Chi-restraints excluded: chain I residue 603 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 700 VAL Chi-restraints excluded: chain I residue 704 MET Chi-restraints excluded: chain I residue 712 SER Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 789 THR Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 805 MET Chi-restraints excluded: chain I residue 823 VAL Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 959 ASP Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1239 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 491 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 682 VAL Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 844 THR Chi-restraints excluded: chain J residue 860 ARG Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1156 LEU Chi-restraints excluded: chain J residue 1189 MET Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1256 ILE Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 170 optimal weight: 0.5980 chunk 288 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 167 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 231 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 GLN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 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 = 0.4527 r_free = 0.4527 target = 0.205232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133181 restraints weight = 44672.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138183 restraints weight = 23804.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.139231 restraints weight = 14404.585| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26089 Z= 0.148 Angle : 0.690 14.220 35444 Z= 0.347 Chirality : 0.044 0.221 4051 Planarity : 0.005 0.067 4467 Dihedral : 14.379 175.104 4035 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 3.66 % Allowed : 23.91 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3124 helix: 0.78 (0.16), residues: 1102 sheet: -0.91 (0.25), residues: 420 loop : -1.50 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I1276 HIS 0.005 0.001 HIS J 777 PHE 0.022 0.001 PHE I 80 TYR 0.019 0.001 TYR H 177 ARG 0.010 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 1046) hydrogen bonds : angle 4.94269 ( 2917) metal coordination : bond 0.00540 ( 8) metal coordination : angle 2.48990 ( 12) covalent geometry : bond 0.00348 (26081) covalent geometry : angle 0.68849 (35432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 503 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 MET cc_start: 0.8947 (mmm) cc_final: 0.8650 (mmm) REVERT: G 71 LYS cc_start: 0.8611 (tptt) cc_final: 0.8371 (tptm) REVERT: G 75 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7842 (pp30) REVERT: G 125 LYS cc_start: 0.8707 (tttt) cc_final: 0.8146 (tttm) REVERT: G 145 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8496 (tppt) REVERT: G 181 GLU cc_start: 0.7272 (mp0) cc_final: 0.6682 (mp0) REVERT: G 206 GLU cc_start: 0.7261 (tp30) cc_final: 0.6619 (tp30) REVERT: H 18 GLN cc_start: 0.8838 (pm20) cc_final: 0.8542 (mp10) REVERT: H 51 MET cc_start: 0.8439 (tpp) cc_final: 0.8140 (tpp) REVERT: H 147 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8414 (tm-30) REVERT: H 219 ARG cc_start: 0.8998 (mmm-85) cc_final: 0.8639 (mmm-85) REVERT: I 37 LYS cc_start: 0.8579 (ttpt) cc_final: 0.7816 (tttm) REVERT: I 97 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7287 (mmm-85) REVERT: I 121 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8497 (tm-30) REVERT: I 122 VAL cc_start: 0.8689 (p) cc_final: 0.8277 (t) REVERT: I 218 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8853 (mt-10) REVERT: I 431 LYS cc_start: 0.8736 (tppt) cc_final: 0.8442 (tppt) REVERT: I 479 LEU cc_start: 0.9292 (tp) cc_final: 0.9091 (pp) REVERT: I 540 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8112 (ttm110) REVERT: I 731 ARG cc_start: 0.7966 (ptp90) cc_final: 0.7405 (ptp90) REVERT: I 865 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.7815 (mt) REVERT: I 951 MET cc_start: 0.9074 (tmm) cc_final: 0.8755 (ppp) REVERT: I 958 LYS cc_start: 0.9332 (tmtt) cc_final: 0.8833 (tptp) REVERT: I 1032 LYS cc_start: 0.9498 (mmtm) cc_final: 0.9294 (mmtm) REVERT: I 1064 ASP cc_start: 0.7684 (t70) cc_final: 0.7422 (t70) REVERT: I 1089 GLU cc_start: 0.8193 (tp30) cc_final: 0.7835 (tp30) REVERT: I 1166 ASP cc_start: 0.8587 (m-30) cc_final: 0.7774 (t0) REVERT: I 1170 MET cc_start: 0.8316 (mmt) cc_final: 0.7877 (mmt) REVERT: I 1174 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8197 (tp30) REVERT: I 1177 ARG cc_start: 0.8263 (ptm-80) cc_final: 0.8053 (ptm160) REVERT: I 1194 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: I 1230 MET cc_start: 0.8766 (ttp) cc_final: 0.8451 (ttt) REVERT: I 1240 ASP cc_start: 0.8617 (p0) cc_final: 0.8357 (t0) REVERT: I 1246 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7699 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8823 (m-80) cc_final: 0.8534 (m-10) REVERT: I 1327 LEU cc_start: 0.7883 (tt) cc_final: 0.7629 (pp) REVERT: I 1332 SER cc_start: 0.6960 (OUTLIER) cc_final: 0.6728 (p) REVERT: J 123 ARG cc_start: 0.7560 (mmm160) cc_final: 0.7120 (mmp80) REVERT: J 189 LEU cc_start: 0.9420 (mp) cc_final: 0.9023 (pp) REVERT: J 298 MET cc_start: 0.5281 (mmt) cc_final: 0.5026 (tmm) REVERT: J 341 ASN cc_start: 0.8265 (m110) cc_final: 0.7433 (m-40) REVERT: J 342 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7121 (mt) REVERT: J 403 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7899 (mmp80) REVERT: J 417 ARG cc_start: 0.8231 (tpt170) cc_final: 0.7691 (mmm160) REVERT: J 449 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.6963 (tp) REVERT: J 504 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: J 646 ILE cc_start: 0.8338 (mm) cc_final: 0.7629 (tp) REVERT: J 739 GLN cc_start: 0.8128 (pt0) cc_final: 0.7900 (pt0) REVERT: J 770 LEU cc_start: 0.8319 (mt) cc_final: 0.8108 (mt) REVERT: J 822 MET cc_start: 0.8227 (tpt) cc_final: 0.7927 (tpt) REVERT: J 844 THR cc_start: 0.8334 (p) cc_final: 0.8090 (t) REVERT: J 1003 LEU cc_start: 0.8330 (tp) cc_final: 0.8079 (tp) REVERT: J 1040 MET cc_start: 0.4900 (mtt) cc_final: 0.2608 (ppp) REVERT: J 1156 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9417 (tp) REVERT: J 1189 MET cc_start: 0.7768 (ttm) cc_final: 0.7021 (tmm) REVERT: J 1372 ARG cc_start: 0.6734 (mmp80) cc_final: 0.6353 (mmp80) REVERT: K 29 GLN cc_start: 0.9125 (mt0) cc_final: 0.8109 (tm-30) REVERT: K 52 ARG cc_start: 0.8578 (mtp180) cc_final: 0.8087 (ptm160) outliers start: 98 outliers final: 74 residues processed: 566 average time/residue: 0.4130 time to fit residues: 356.5082 Evaluate side-chains 554 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 471 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 455 SER Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 757 THR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain I residue 1332 SER Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1156 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1239 ASP Chi-restraints excluded: chain J residue 1283 SER Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 101 optimal weight: 3.9990 chunk 128 optimal weight: 0.0770 chunk 98 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 195 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 278 optimal weight: 0.0770 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 339 ASN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 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 = 0.4554 r_free = 0.4554 target = 0.208057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141876 restraints weight = 44592.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.143025 restraints weight = 26149.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144011 restraints weight = 16837.339| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26089 Z= 0.128 Angle : 0.693 15.289 35444 Z= 0.346 Chirality : 0.043 0.245 4051 Planarity : 0.005 0.065 4467 Dihedral : 14.270 174.361 4035 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 3.18 % Allowed : 24.77 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3124 helix: 0.75 (0.16), residues: 1101 sheet: -0.72 (0.25), residues: 413 loop : -1.46 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I1276 HIS 0.006 0.001 HIS I 150 PHE 0.033 0.001 PHE I 337 TYR 0.016 0.001 TYR I 742 ARG 0.009 0.000 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 1046) hydrogen bonds : angle 4.81417 ( 2917) metal coordination : bond 0.00295 ( 8) metal coordination : angle 1.86258 ( 12) covalent geometry : bond 0.00294 (26081) covalent geometry : angle 0.69192 (35432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 509 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 33 ARG cc_start: 0.7576 (tpp80) cc_final: 0.7163 (mmt-90) REVERT: G 51 MET cc_start: 0.8871 (mmm) cc_final: 0.8579 (mmm) REVERT: G 58 GLU cc_start: 0.7582 (tt0) cc_final: 0.7323 (tt0) REVERT: G 71 LYS cc_start: 0.8447 (tptt) cc_final: 0.8186 (tptm) REVERT: G 125 LYS cc_start: 0.8737 (tttt) cc_final: 0.8214 (tttm) REVERT: G 145 LYS cc_start: 0.8599 (ttmm) cc_final: 0.8382 (tppt) REVERT: G 181 GLU cc_start: 0.7172 (mp0) cc_final: 0.6779 (mp0) REVERT: G 206 GLU cc_start: 0.7260 (tp30) cc_final: 0.6845 (tp30) REVERT: H 18 GLN cc_start: 0.8784 (pm20) cc_final: 0.8489 (mp10) REVERT: H 51 MET cc_start: 0.8311 (tpp) cc_final: 0.8013 (tpp) REVERT: H 147 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8425 (tm-30) REVERT: H 200 LYS cc_start: 0.7812 (tttm) cc_final: 0.7598 (tptt) REVERT: H 219 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8538 (mmm-85) REVERT: I 37 LYS cc_start: 0.8458 (ttpt) cc_final: 0.7834 (tttm) REVERT: I 97 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7358 (mmm-85) REVERT: I 121 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8486 (tm-30) REVERT: I 122 VAL cc_start: 0.8599 (p) cc_final: 0.8102 (t) REVERT: I 218 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8736 (pp20) REVERT: I 365 GLU cc_start: 0.8200 (tp30) cc_final: 0.7989 (tp30) REVERT: I 431 LYS cc_start: 0.8656 (tppt) cc_final: 0.8410 (tppt) REVERT: I 524 ILE cc_start: 0.9347 (tp) cc_final: 0.9101 (tp) REVERT: I 540 ARG cc_start: 0.8327 (ttm110) cc_final: 0.8094 (ttm110) REVERT: I 575 LEU cc_start: 0.8667 (tp) cc_final: 0.7921 (mt) REVERT: I 674 ASP cc_start: 0.8534 (p0) cc_final: 0.8146 (p0) REVERT: I 731 ARG cc_start: 0.7896 (ptp90) cc_final: 0.7468 (ptp90) REVERT: I 790 ASP cc_start: 0.8599 (p0) cc_final: 0.8379 (p0) REVERT: I 865 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7588 (mt) REVERT: I 958 LYS cc_start: 0.9265 (tmtt) cc_final: 0.8820 (tptp) REVERT: I 1089 GLU cc_start: 0.8137 (tp30) cc_final: 0.7746 (tp30) REVERT: I 1166 ASP cc_start: 0.8614 (m-30) cc_final: 0.7885 (t0) REVERT: I 1170 MET cc_start: 0.8256 (mmt) cc_final: 0.7879 (mmt) REVERT: I 1174 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8033 (tp30) REVERT: I 1230 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8370 (ttt) REVERT: I 1246 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7779 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8730 (m-80) cc_final: 0.8492 (m-10) REVERT: I 1327 LEU cc_start: 0.7935 (tt) cc_final: 0.7669 (pp) REVERT: J 189 LEU cc_start: 0.9365 (mp) cc_final: 0.8985 (pp) REVERT: J 237 MET cc_start: 0.6426 (mpp) cc_final: 0.6093 (mpp) REVERT: J 298 MET cc_start: 0.5859 (mmt) cc_final: 0.5510 (tmm) REVERT: J 330 MET cc_start: 0.7053 (tpp) cc_final: 0.6832 (tpp) REVERT: J 341 ASN cc_start: 0.8199 (m110) cc_final: 0.7616 (m-40) REVERT: J 342 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7139 (mt) REVERT: J 417 ARG cc_start: 0.7981 (tpt170) cc_final: 0.7442 (mmm160) REVERT: J 449 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7314 (tp) REVERT: J 490 ILE cc_start: 0.9353 (pt) cc_final: 0.8893 (mt) REVERT: J 504 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6248 (pt0) REVERT: J 604 MET cc_start: 0.7821 (ttt) cc_final: 0.7605 (ttt) REVERT: J 646 ILE cc_start: 0.8108 (mm) cc_final: 0.7337 (tp) REVERT: J 821 MET cc_start: 0.8314 (mmm) cc_final: 0.8013 (tpp) REVERT: J 891 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7230 (t0) REVERT: J 1003 LEU cc_start: 0.8288 (tp) cc_final: 0.8056 (tp) REVERT: J 1040 MET cc_start: 0.4765 (mtt) cc_final: 0.2436 (ppp) REVERT: J 1189 MET cc_start: 0.7594 (ttm) cc_final: 0.6929 (tmm) REVERT: J 1320 ILE cc_start: 0.8660 (mm) cc_final: 0.8417 (mm) REVERT: J 1372 ARG cc_start: 0.7028 (mmp80) cc_final: 0.6684 (mmp80) REVERT: K 29 GLN cc_start: 0.9053 (mt0) cc_final: 0.7934 (tm-30) REVERT: K 30 MET cc_start: 0.7527 (mmt) cc_final: 0.6831 (mmm) REVERT: K 52 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8334 (mtp180) outliers start: 85 outliers final: 60 residues processed: 564 average time/residue: 0.4181 time to fit residues: 359.0107 Evaluate side-chains 540 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 473 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 211 ARG Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1026 GLU Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 694 SER Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 817 HIS Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 82 optimal weight: 0.8980 chunk 280 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 242 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1090 ASN J 157 GLN ** J 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 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 = 0.4542 r_free = 0.4542 target = 0.206885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.136049 restraints weight = 44762.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140786 restraints weight = 24375.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.142567 restraints weight = 14835.819| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26089 Z= 0.149 Angle : 0.724 14.459 35444 Z= 0.358 Chirality : 0.044 0.255 4051 Planarity : 0.005 0.065 4467 Dihedral : 14.248 174.151 4031 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.44 % Favored : 94.53 % Rotamer: Outliers : 3.29 % Allowed : 24.77 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3124 helix: 0.75 (0.16), residues: 1104 sheet: -0.63 (0.26), residues: 411 loop : -1.45 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I1276 HIS 0.005 0.001 HIS I 150 PHE 0.026 0.001 PHE I 337 TYR 0.031 0.001 TYR I 291 ARG 0.013 0.001 ARG I1033 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1046) hydrogen bonds : angle 4.80751 ( 2917) metal coordination : bond 0.00488 ( 8) metal coordination : angle 1.68744 ( 12) covalent geometry : bond 0.00352 (26081) covalent geometry : angle 0.72327 (35432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 486 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 35 PHE cc_start: 0.8435 (m-80) cc_final: 0.7867 (m-80) REVERT: G 51 MET cc_start: 0.8928 (mmm) cc_final: 0.8590 (mmm) REVERT: G 71 LYS cc_start: 0.8519 (tptt) cc_final: 0.8255 (tptm) REVERT: G 125 LYS cc_start: 0.8774 (tttt) cc_final: 0.8247 (tttm) REVERT: G 181 GLU cc_start: 0.7225 (mp0) cc_final: 0.6694 (mp0) REVERT: G 206 GLU cc_start: 0.7225 (tp30) cc_final: 0.6590 (tp30) REVERT: G 227 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8946 (mm-40) REVERT: H 18 GLN cc_start: 0.8798 (pm20) cc_final: 0.8473 (mp10) REVERT: H 51 MET cc_start: 0.8460 (tpp) cc_final: 0.8127 (tpp) REVERT: H 147 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8359 (tm-30) REVERT: H 200 LYS cc_start: 0.7876 (tttm) cc_final: 0.7534 (tptt) REVERT: H 219 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8625 (mmm-85) REVERT: I 37 LYS cc_start: 0.8499 (ttpt) cc_final: 0.7693 (tttm) REVERT: I 97 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7119 (mmm-85) REVERT: I 121 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8443 (tm-30) REVERT: I 187 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7756 (mm-30) REVERT: I 202 ARG cc_start: 0.7786 (mmt-90) cc_final: 0.7353 (mmt180) REVERT: I 218 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8759 (mt-10) REVERT: I 369 MET cc_start: 0.8633 (mmm) cc_final: 0.8344 (mmp) REVERT: I 394 ARG cc_start: 0.7995 (tpt170) cc_final: 0.7597 (tpt170) REVERT: I 431 LYS cc_start: 0.8731 (tppt) cc_final: 0.8449 (tppt) REVERT: I 540 ARG cc_start: 0.8369 (ttm110) cc_final: 0.8101 (ttm110) REVERT: I 731 ARG cc_start: 0.8067 (ptp90) cc_final: 0.7500 (ptp90) REVERT: I 865 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7563 (mt) REVERT: I 951 MET cc_start: 0.8400 (ppp) cc_final: 0.8111 (ppp) REVERT: I 958 LYS cc_start: 0.9309 (tmtt) cc_final: 0.8837 (tptp) REVERT: I 1089 GLU cc_start: 0.8166 (tp30) cc_final: 0.7785 (tp30) REVERT: I 1166 ASP cc_start: 0.8633 (m-30) cc_final: 0.7887 (t0) REVERT: I 1170 MET cc_start: 0.8273 (mmt) cc_final: 0.7912 (mmt) REVERT: I 1174 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8066 (tp30) REVERT: I 1230 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8446 (ttt) REVERT: I 1246 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7708 (ttm-80) REVERT: I 1281 TYR cc_start: 0.8839 (m-80) cc_final: 0.8581 (m-10) REVERT: I 1327 LEU cc_start: 0.7879 (tt) cc_final: 0.7644 (pp) REVERT: J 37 GLU cc_start: 0.7938 (tp30) cc_final: 0.7616 (tp30) REVERT: J 123 ARG cc_start: 0.6985 (mmm160) cc_final: 0.6570 (mmp80) REVERT: J 189 LEU cc_start: 0.9419 (mp) cc_final: 0.9020 (pp) REVERT: J 341 ASN cc_start: 0.8510 (m110) cc_final: 0.7903 (t0) REVERT: J 342 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7114 (mt) REVERT: J 403 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7936 (mmp80) REVERT: J 417 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7576 (mmm160) REVERT: J 449 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7312 (tp) REVERT: J 553 THR cc_start: 0.8940 (m) cc_final: 0.8609 (p) REVERT: J 697 MET cc_start: 0.8378 (tmm) cc_final: 0.7710 (tmm) REVERT: J 821 MET cc_start: 0.8577 (mmm) cc_final: 0.8288 (tpp) REVERT: J 891 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7335 (t0) REVERT: J 1003 LEU cc_start: 0.8360 (tp) cc_final: 0.8110 (tp) REVERT: J 1040 MET cc_start: 0.4786 (mtt) cc_final: 0.2557 (ppp) REVERT: J 1155 ILE cc_start: 0.9367 (mm) cc_final: 0.9140 (tp) REVERT: J 1189 MET cc_start: 0.7880 (ttm) cc_final: 0.7122 (tmm) REVERT: J 1372 ARG cc_start: 0.7034 (mmp80) cc_final: 0.6688 (mmp80) REVERT: K 29 GLN cc_start: 0.9124 (mt0) cc_final: 0.8110 (tm-30) REVERT: K 52 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8284 (mtp180) REVERT: K 61 ASN cc_start: 0.8333 (t0) cc_final: 0.8065 (p0) outliers start: 88 outliers final: 68 residues processed: 546 average time/residue: 0.4117 time to fit residues: 342.1218 Evaluate side-chains 537 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 463 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 346 TYR Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 630 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 862 LEU Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1230 MET Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 374 LEU Chi-restraints excluded: chain J residue 425 ARG Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 737 ILE Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 45 optimal weight: 0.0370 chunk 141 optimal weight: 20.0000 chunk 163 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 298 optimal weight: 0.0000 chunk 125 optimal weight: 0.3980 chunk 299 optimal weight: 0.9990 chunk 274 optimal weight: 0.5980 chunk 95 optimal weight: 0.0370 chunk 43 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 overall best weight: 0.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 GLN ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 450 HIS J 720 ASN J 921 GLN ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.210176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.146158 restraints weight = 44698.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.147027 restraints weight = 25584.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.147212 restraints weight = 18014.396| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26089 Z= 0.130 Angle : 0.745 14.439 35444 Z= 0.366 Chirality : 0.044 0.259 4051 Planarity : 0.005 0.094 4467 Dihedral : 14.208 174.210 4031 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 2.80 % Allowed : 25.70 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3124 helix: 0.67 (0.16), residues: 1114 sheet: -0.65 (0.26), residues: 405 loop : -1.47 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I1276 HIS 0.005 0.001 HIS I 150 PHE 0.025 0.001 PHE I 337 TYR 0.021 0.001 TYR J 382 ARG 0.016 0.001 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 1046) hydrogen bonds : angle 4.70645 ( 2917) metal coordination : bond 0.00175 ( 8) metal coordination : angle 1.57195 ( 12) covalent geometry : bond 0.00300 (26081) covalent geometry : angle 0.74474 (35432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6248 Ramachandran restraints generated. 3124 Oldfield, 0 Emsley, 3124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 507 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 51 MET cc_start: 0.8863 (mmm) cc_final: 0.8627 (mmm) REVERT: G 71 LYS cc_start: 0.8424 (tptt) cc_final: 0.8219 (tptm) REVERT: G 125 LYS cc_start: 0.8781 (tttt) cc_final: 0.8379 (tttm) REVERT: G 145 LYS cc_start: 0.8520 (tppt) cc_final: 0.8217 (tptp) REVERT: G 181 GLU cc_start: 0.7127 (mp0) cc_final: 0.6817 (mp0) REVERT: G 199 ASP cc_start: 0.6965 (m-30) cc_final: 0.6556 (m-30) REVERT: G 206 GLU cc_start: 0.7240 (tp30) cc_final: 0.6853 (tp30) REVERT: G 227 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8924 (mm-40) REVERT: H 18 GLN cc_start: 0.8771 (pm20) cc_final: 0.8455 (mp10) REVERT: H 51 MET cc_start: 0.8301 (tpp) cc_final: 0.8017 (tpp) REVERT: H 147 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8321 (tm-30) REVERT: H 219 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8568 (mmm-85) REVERT: I 187 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7762 (mm-30) REVERT: I 218 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8746 (mt-10) REVERT: I 319 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8760 (pt) REVERT: I 369 MET cc_start: 0.8835 (mmm) cc_final: 0.8466 (tpt) REVERT: I 394 ARG cc_start: 0.7938 (tpt170) cc_final: 0.7517 (tpt170) REVERT: I 431 LYS cc_start: 0.8603 (tppt) cc_final: 0.8348 (tppt) REVERT: I 517 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6875 (pt0) REVERT: I 524 ILE cc_start: 0.9327 (tp) cc_final: 0.9074 (tp) REVERT: I 540 ARG cc_start: 0.8306 (ttm110) cc_final: 0.8096 (ttm110) REVERT: I 674 ASP cc_start: 0.8601 (p0) cc_final: 0.8302 (p0) REVERT: I 693 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7248 (mp) REVERT: I 731 ARG cc_start: 0.8046 (ptp90) cc_final: 0.7554 (ptp90) REVERT: I 865 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7323 (mt) REVERT: I 951 MET cc_start: 0.8287 (ppp) cc_final: 0.8003 (ppp) REVERT: I 958 LYS cc_start: 0.9287 (tmtt) cc_final: 0.8777 (tptp) REVERT: I 1089 GLU cc_start: 0.8132 (tp30) cc_final: 0.7689 (tp30) REVERT: I 1166 ASP cc_start: 0.8661 (m-30) cc_final: 0.7985 (t0) REVERT: I 1170 MET cc_start: 0.8228 (mmt) cc_final: 0.7881 (mmt) REVERT: I 1174 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7978 (tp30) REVERT: I 1246 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7470 (ttm-80) REVERT: I 1327 LEU cc_start: 0.7920 (tt) cc_final: 0.7677 (pp) REVERT: J 123 ARG cc_start: 0.6931 (mmm160) cc_final: 0.6533 (mmp80) REVERT: J 180 MET cc_start: 0.7467 (tpt) cc_final: 0.7009 (tpp) REVERT: J 189 LEU cc_start: 0.9433 (mp) cc_final: 0.9052 (pp) REVERT: J 237 MET cc_start: 0.6665 (mpp) cc_final: 0.6363 (mpp) REVERT: J 298 MET cc_start: 0.6012 (mmt) cc_final: 0.5665 (tmm) REVERT: J 341 ASN cc_start: 0.8382 (m110) cc_final: 0.7640 (m-40) REVERT: J 342 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7032 (mt) REVERT: J 403 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7869 (mmp80) REVERT: J 404 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7765 (tm-30) REVERT: J 409 TRP cc_start: 0.8316 (m100) cc_final: 0.7929 (m100) REVERT: J 417 ARG cc_start: 0.7922 (tpt170) cc_final: 0.7435 (mmm160) REVERT: J 441 LEU cc_start: 0.9219 (mt) cc_final: 0.8981 (mp) REVERT: J 449 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7316 (tp) REVERT: J 553 THR cc_start: 0.8865 (m) cc_final: 0.8545 (p) REVERT: J 646 ILE cc_start: 0.7993 (mm) cc_final: 0.7557 (tp) REVERT: J 821 MET cc_start: 0.8503 (mmm) cc_final: 0.8141 (tpp) REVERT: J 891 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7141 (t0) REVERT: J 1003 LEU cc_start: 0.8347 (tp) cc_final: 0.8117 (tp) REVERT: J 1040 MET cc_start: 0.4815 (mtt) cc_final: 0.2448 (ppp) REVERT: J 1155 ILE cc_start: 0.9303 (mm) cc_final: 0.9084 (tp) REVERT: J 1189 MET cc_start: 0.7705 (ttm) cc_final: 0.6985 (tmm) REVERT: J 1372 ARG cc_start: 0.7076 (mmp80) cc_final: 0.6754 (mmp80) REVERT: K 29 GLN cc_start: 0.9125 (mt0) cc_final: 0.8110 (tm-30) REVERT: K 52 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8297 (mtp180) REVERT: K 61 ASN cc_start: 0.8292 (t0) cc_final: 0.8082 (p0) outliers start: 75 outliers final: 55 residues processed: 555 average time/residue: 0.4260 time to fit residues: 360.9433 Evaluate side-chains 530 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 467 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain H residue 142 MET Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 517 GLN Chi-restraints excluded: chain I residue 615 VAL Chi-restraints excluded: chain I residue 623 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 850 ILE Chi-restraints excluded: chain I residue 865 LEU Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 884 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 922 ASN Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1109 ILE Chi-restraints excluded: chain I residue 1246 ARG Chi-restraints excluded: chain I residue 1278 LEU Chi-restraints excluded: chain I residue 1328 LYS Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 430 HIS Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 501 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 639 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 740 LEU Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 882 VAL Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 8 optimal weight: 5.9990 chunk 274 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 201 optimal weight: 0.2980 chunk 246 optimal weight: 0.9980 chunk 232 optimal weight: 0.6980 chunk 180 optimal weight: 40.0000 chunk 47 optimal weight: 0.0030 chunk 16 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.210030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.156572 restraints weight = 44710.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.153899 restraints weight = 28966.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.155333 restraints weight = 27528.459| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26089 Z= 0.134 Angle : 0.754 14.381 35444 Z= 0.371 Chirality : 0.045 0.310 4051 Planarity : 0.005 0.079 4467 Dihedral : 14.199 174.037 4031 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 2.39 % Allowed : 26.78 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3124 helix: 0.66 (0.16), residues: 1108 sheet: -0.55 (0.26), residues: 401 loop : -1.43 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I1276 HIS 0.005 0.001 HIS I 150 PHE 0.023 0.001 PHE I 337 TYR 0.017 0.001 TYR J 382 ARG 0.014 0.001 ARG K 67 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1046) hydrogen bonds : angle 4.74215 ( 2917) metal coordination : bond 0.00227 ( 8) metal coordination : angle 1.41721 ( 12) covalent geometry : bond 0.00311 (26081) covalent geometry : angle 0.75336 (35432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10112.25 seconds wall clock time: 175 minutes 8.99 seconds (10508.99 seconds total)