Starting phenix.real_space_refine on Mon Aug 25 05:58:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t02_40931/08_2025/8t02_40931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t02_40931/08_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_40931/08_2025/8t02_40931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t02_40931/08_2025/8t02_40931.map" model { file = "/net/cci-nas-00/data/ceres_data/8t02_40931/08_2025/8t02_40931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t02_40931/08_2025/8t02_40931.cif" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLN:plan1': 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: 6.23, per 1000 atoms: 0.24 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: 2.57 Conformation dependent library (CDL) restraints added in 978.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 3.37 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: 6.83 Time building geometry restraints manager: 3.26 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 32.430 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.220 ------------------------------------------------------------------------------- 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 : 9.26 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.014 0.000 ARG I1033 TYR 0.024 0.001 TYR I1229 PHE 0.017 0.001 PHE I 230 TRP 0.011 0.001 TRP J 236 HIS 0.005 0.001 HIS J1366 Details of bonding type rmsd covalent geometry : bond 0.00350 (26081) covalent geometry : angle 0.60965 (35432) hydrogen bonds : bond 0.15933 ( 1046) hydrogen bonds : angle 6.49414 ( 2917) metal coordination : bond 0.04809 ( 8) metal coordination : angle 34.94997 ( 12) *********************** 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 : 1.022 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: 0.1889 time to fit residues: 217.6791 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 : 0.610 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.0870 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 659 GLN I 952 GLN I1146 GLN I1220 GLN J 157 GLN J 865 HIS 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 = 0.4557 r_free = 0.4557 target = 0.208621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.142641 restraints weight = 44813.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143135 restraints weight = 26214.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.143564 restraints weight = 18777.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.144329 restraints weight = 17608.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145269 restraints weight = 15379.056| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26089 Z= 0.150 Angle : 0.725 17.348 35444 Z= 0.359 Chirality : 0.045 0.237 4051 Planarity : 0.005 0.079 4467 Dihedral : 14.472 175.786 4068 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 3.55 % Allowed : 18.30 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3124 helix: 0.80 (0.16), residues: 1105 sheet: -0.96 (0.24), residues: 394 loop : -1.62 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 12 TYR 0.015 0.001 TYR J 772 PHE 0.020 0.001 PHE I 80 TRP 0.022 0.002 TRP I 997 HIS 0.005 0.001 HIS G 23 Details of bonding type rmsd covalent geometry : bond 0.00335 (26081) covalent geometry : angle 0.70059 (35432) hydrogen bonds : bond 0.04381 ( 1046) hydrogen bonds : angle 5.26943 ( 2917) metal coordination : bond 0.01428 ( 8) metal coordination : angle 10.05967 ( 12) *********************** 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 698 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 603 time to evaluate : 1.015 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 51 MET cc_start: 0.8879 (mmm) cc_final: 0.8606 (mmm) REVERT: G 58 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7098 (mt-10) REVERT: G 71 LYS cc_start: 0.8455 (tptt) cc_final: 0.8064 (tptm) REVERT: G 120 ASP cc_start: 0.7535 (p0) cc_final: 0.6684 (t70) REVERT: G 125 LYS cc_start: 0.8622 (tttt) cc_final: 0.8177 (tttm) REVERT: G 181 GLU cc_start: 0.7232 (mp0) cc_final: 0.6727 (mp0) REVERT: G 199 ASP cc_start: 0.7528 (m-30) cc_final: 0.7051 (m-30) REVERT: G 206 GLU cc_start: 0.6941 (tp30) cc_final: 0.6551 (tp30) REVERT: I 8 LYS cc_start: 0.9016 (mttt) cc_final: 0.8528 (mttm) REVERT: I 37 LYS cc_start: 0.8508 (ttpt) cc_final: 0.8168 (tptt) REVERT: I 97 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7137 (mmm-85) REVERT: I 121 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8272 (tm-30) REVERT: I 130 MET cc_start: 0.8210 (ttm) cc_final: 0.7954 (ttm) REVERT: I 369 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8542 (ppp) REVERT: I 384 LEU cc_start: 0.8656 (tt) cc_final: 0.8368 (mt) REVERT: I 524 ILE cc_start: 0.9191 (tp) cc_final: 0.8971 (tp) REVERT: I 575 LEU cc_start: 0.8737 (tp) cc_final: 0.8017 (mt) REVERT: I 653 MET cc_start: 0.7924 (tpp) cc_final: 0.7633 (tpt) REVERT: I 731 ARG cc_start: 0.7825 (ptp90) cc_final: 0.7444 (ptp90) REVERT: I 932 GLN cc_start: 0.6211 (tp40) cc_final: 0.5947 (tp40) REVERT: I 933 VAL cc_start: 0.7948 (t) cc_final: 0.7406 (t) REVERT: I 958 LYS cc_start: 0.9170 (tmtt) cc_final: 0.8622 (tptp) REVERT: I 1072 ASN cc_start: 0.8507 (p0) cc_final: 0.8170 (p0) REVERT: I 1089 GLU cc_start: 0.8144 (tp30) cc_final: 0.7757 (tp30) REVERT: I 1090 ASN cc_start: 0.8698 (t0) cc_final: 0.8483 (t0) REVERT: I 1166 ASP cc_start: 0.8548 (m-30) cc_final: 0.7891 (t0) REVERT: I 1170 MET cc_start: 0.8157 (mmt) cc_final: 0.7790 (mmt) REVERT: I 1174 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8150 (tp30) REVERT: I 1229 TYR cc_start: 0.8333 (m-10) cc_final: 0.8108 (m-10) REVERT: I 1240 ASP cc_start: 0.8548 (p0) cc_final: 0.7670 (t0) REVERT: I 1241 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8178 (t0) REVERT: I 1281 TYR cc_start: 0.8720 (m-80) cc_final: 0.8391 (m-10) REVERT: I 1290 MET cc_start: 0.8411 (tpp) cc_final: 0.7938 (tpp) REVERT: I 1304 MET cc_start: 0.7675 (ttm) cc_final: 0.7405 (ttm) REVERT: J 298 MET cc_start: 0.5789 (mmt) cc_final: 0.5470 (tmm) REVERT: J 403 ARG cc_start: 0.8271 (mmp80) cc_final: 0.8058 (mmp80) REVERT: J 449 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7425 (tp) REVERT: J 462 ASP cc_start: 0.8211 (p0) cc_final: 0.7928 (p0) REVERT: J 521 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8140 (mtpp) REVERT: J 553 THR cc_start: 0.8965 (m) cc_final: 0.8553 (p) REVERT: J 739 GLN cc_start: 0.8333 (pt0) cc_final: 0.8024 (pt0) REVERT: J 891 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7259 (t0) REVERT: J 1003 LEU cc_start: 0.8070 (tp) cc_final: 0.7730 (tp) REVERT: J 1040 MET cc_start: 0.4101 (mtt) cc_final: 0.1026 (ppp) REVERT: J 1189 MET cc_start: 0.7589 (ttm) cc_final: 0.7069 (tmm) REVERT: K 61 ASN cc_start: 0.8468 (m-40) cc_final: 0.8116 (t0) REVERT: K 63 ILE cc_start: 0.8499 (tp) cc_final: 0.8283 (pt) outliers start: 95 outliers final: 43 residues processed: 662 average time/residue: 0.1989 time to fit residues: 200.2858 Evaluate side-chains 554 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 506 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE 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 50 SER Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 122 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 158 ASP Chi-restraints excluded: chain I residue 369 MET 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 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 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 1239 ASP 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 178 optimal weight: 20.0000 chunk 139 optimal weight: 50.0000 chunk 62 optimal weight: 8.9990 chunk 278 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 198 optimal weight: 30.0000 chunk 110 optimal weight: 0.6980 chunk 286 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 430 HIS J 465 GLN ** J 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.200467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.124547 restraints weight = 44786.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.129357 restraints weight = 25558.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.129926 restraints weight = 16497.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.130676 restraints weight = 15029.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130784 restraints weight = 14781.025| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 26089 Z= 0.372 Angle : 0.837 18.384 35444 Z= 0.426 Chirality : 0.048 0.261 4051 Planarity : 0.007 0.120 4467 Dihedral : 14.576 179.793 4039 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.39 % Favored : 92.54 % Rotamer: Outliers : 5.12 % Allowed : 18.60 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 1.57 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.14), residues: 3124 helix: 0.47 (0.15), residues: 1113 sheet: -1.00 (0.24), residues: 415 loop : -1.71 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 211 TYR 0.026 0.002 TYR J 772 PHE 0.024 0.002 PHE I1187 TRP 0.029 0.003 TRP I 997 HIS 0.009 0.002 HIS I 447 Details of bonding type rmsd covalent geometry : bond 0.00852 (26081) covalent geometry : angle 0.82465 (35432) hydrogen bonds : bond 0.05000 ( 1046) hydrogen bonds : angle 5.55372 ( 2917) metal coordination : bond 0.02090 ( 8) metal coordination : angle 7.97872 ( 12) *********************** 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 645 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 508 time to evaluate : 1.030 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 10 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7015 (mmtm) REVERT: G 35 PHE cc_start: 0.8514 (m-80) cc_final: 0.7971 (m-80) REVERT: G 125 LYS cc_start: 0.8662 (tttt) cc_final: 0.8020 (tttm) REVERT: G 206 GLU cc_start: 0.6942 (tp30) cc_final: 0.6685 (tp30) REVERT: H 18 GLN cc_start: 0.8889 (pm20) cc_final: 0.8555 (mp10) REVERT: H 147 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8110 (tm-30) REVERT: H 152 TYR cc_start: 0.7402 (t80) cc_final: 0.7120 (t80) REVERT: H 177 TYR cc_start: 0.8429 (m-10) cc_final: 0.7900 (m-10) REVERT: I 8 LYS cc_start: 0.9148 (mttt) cc_final: 0.8524 (mttm) REVERT: I 37 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8142 (tptt) REVERT: I 97 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7132 (mmm-85) REVERT: I 121 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8282 (tm-30) REVERT: I 133 ASN cc_start: 0.8036 (t0) cc_final: 0.7701 (t0) REVERT: I 202 ARG cc_start: 0.8505 (ptt180) cc_final: 0.8135 (ptt180) REVERT: I 369 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (ppp) REVERT: I 432 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8806 (tt) REVERT: I 731 ARG cc_start: 0.8099 (ptp90) cc_final: 0.7612 (ptp90) REVERT: I 820 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: I 932 GLN cc_start: 0.6583 (tp40) cc_final: 0.6182 (tp40) REVERT: I 951 MET cc_start: 0.9087 (tmm) cc_final: 0.8729 (ppp) REVERT: I 958 LYS cc_start: 0.9334 (tmtt) cc_final: 0.8935 (tptp) REVERT: I 1089 GLU cc_start: 0.8321 (tp30) cc_final: 0.8006 (tp30) REVERT: I 1166 ASP cc_start: 0.8626 (m-30) cc_final: 0.7718 (t0) REVERT: I 1170 MET cc_start: 0.8322 (mmt) cc_final: 0.7950 (mmt) REVERT: I 1174 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8125 (tp30) REVERT: I 1178 LYS cc_start: 0.8818 (tppp) cc_final: 0.8417 (tppp) REVERT: I 1194 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: I 1230 MET cc_start: 0.8846 (ttp) cc_final: 0.8459 (ttt) REVERT: I 1240 ASP cc_start: 0.8860 (p0) cc_final: 0.8280 (t70) REVERT: I 1281 TYR cc_start: 0.9017 (m-80) cc_final: 0.8494 (m-10) REVERT: I 1304 MET cc_start: 0.7871 (ttm) cc_final: 0.7567 (ttm) REVERT: J 37 GLU cc_start: 0.7976 (tp30) cc_final: 0.7750 (tp30) REVERT: J 102 MET cc_start: 0.8059 (ttt) cc_final: 0.7688 (tpp) REVERT: J 123 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7332 (mmp80) REVERT: J 341 ASN cc_start: 0.8721 (m110) cc_final: 0.7557 (t0) REVERT: J 400 MET cc_start: 0.7843 (mmm) cc_final: 0.7551 (mmm) REVERT: J 417 ARG cc_start: 0.8349 (tpt170) cc_final: 0.7948 (mmm-85) REVERT: J 449 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (mt) REVERT: J 543 SER cc_start: 0.8814 (OUTLIER) cc_final: 0.8370 (p) REVERT: J 844 THR cc_start: 0.8546 (p) cc_final: 0.8292 (t) REVERT: J 891 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.7757 (t0) REVERT: J 1003 LEU cc_start: 0.8084 (tp) cc_final: 0.7796 (tp) REVERT: J 1040 MET cc_start: 0.4545 (mtt) cc_final: 0.1679 (ppp) REVERT: J 1189 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7302 (tmm) REVERT: J 1297 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8180 (pttm) REVERT: K 61 ASN cc_start: 0.8670 (m-40) cc_final: 0.8117 (t0) outliers start: 137 outliers final: 92 residues processed: 599 average time/residue: 0.2008 time to fit residues: 183.2295 Evaluate side-chains 564 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 462 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 LYS 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 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 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 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 224 PHE 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 432 LEU 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 603 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 700 VAL 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 820 GLU 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 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER Chi-restraints excluded: chain I residue 1232 MET Chi-restraints excluded: chain I residue 1241 ASP 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 374 LEU Chi-restraints excluded: chain J residue 408 VAL 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 470 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 507 VAL Chi-restraints excluded: chain J residue 543 SER Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 705 THR Chi-restraints excluded: chain J residue 728 SER Chi-restraints excluded: chain J residue 737 ILE 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 867 GLN Chi-restraints excluded: chain J residue 891 ASP Chi-restraints excluded: chain J residue 892 PHE 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 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 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1297 LYS 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 161 optimal weight: 0.8980 chunk 221 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 162 optimal weight: 0.6980 chunk 96 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 GLN I 120 GLN I 276 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 ASN I1023 HIS I1090 ASN ** 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 = 0.4549 r_free = 0.4549 target = 0.207352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137802 restraints weight = 44427.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140176 restraints weight = 26944.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.141030 restraints weight = 17436.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.141945 restraints weight = 15470.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141970 restraints weight = 14264.552| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26089 Z= 0.140 Angle : 0.697 13.487 35444 Z= 0.349 Chirality : 0.044 0.239 4051 Planarity : 0.005 0.097 4467 Dihedral : 14.417 178.052 4037 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.15 % Favored : 94.81 % Rotamer: Outliers : 3.14 % Allowed : 20.96 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.14), residues: 3124 helix: 0.69 (0.16), residues: 1104 sheet: -0.78 (0.25), residues: 384 loop : -1.61 (0.14), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 540 TYR 0.029 0.001 TYR I 742 PHE 0.014 0.001 PHE J1319 TRP 0.014 0.001 TRP I 997 HIS 0.011 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00321 (26081) covalent geometry : angle 0.69327 (35432) hydrogen bonds : bond 0.04015 ( 1046) hydrogen bonds : angle 5.02908 ( 2917) metal coordination : bond 0.00688 ( 8) metal coordination : angle 3.87575 ( 12) *********************** 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 641 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 557 time to evaluate : 0.980 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: G 10 LYS cc_start: 0.8341 (mmtm) cc_final: 0.7516 (mmtm) REVERT: G 35 PHE cc_start: 0.8441 (m-80) cc_final: 0.7873 (m-80) REVERT: G 51 MET cc_start: 0.8910 (mmm) cc_final: 0.8638 (mmm) REVERT: G 71 LYS cc_start: 0.8547 (tptt) cc_final: 0.8202 (tptm) REVERT: G 75 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7992 (pp30) REVERT: G 125 LYS cc_start: 0.8627 (tttt) cc_final: 0.7983 (tttm) REVERT: G 181 GLU cc_start: 0.7250 (mp0) cc_final: 0.6629 (mp0) REVERT: G 186 ASN cc_start: 0.8513 (OUTLIER) cc_final: 0.7938 (p0) REVERT: G 188 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7606 (mp0) REVERT: G 206 GLU cc_start: 0.7146 (tp30) cc_final: 0.6748 (tp30) REVERT: H 18 GLN cc_start: 0.8888 (pm20) cc_final: 0.8586 (mp10) REVERT: H 132 HIS cc_start: 0.7531 (m-70) cc_final: 0.7284 (m-70) REVERT: I 37 LYS cc_start: 0.8576 (ttpt) cc_final: 0.8003 (tptm) REVERT: I 97 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7159 (mmm-85) REVERT: I 121 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8407 (tm-30) REVERT: I 151 ARG cc_start: 0.8125 (ttt-90) cc_final: 0.7873 (mtp85) REVERT: I 202 ARG cc_start: 0.8541 (ptt180) cc_final: 0.8166 (ptt180) REVERT: I 211 ARG cc_start: 0.8642 (ptt180) cc_final: 0.8394 (ptt180) REVERT: I 363 LEU cc_start: 0.9334 (mt) cc_final: 0.9121 (tp) REVERT: I 524 ILE cc_start: 0.9295 (tp) cc_final: 0.9072 (tp) REVERT: I 575 LEU cc_start: 0.8637 (tp) cc_final: 0.8069 (mt) REVERT: I 653 MET cc_start: 0.7919 (tpp) cc_final: 0.7201 (tpt) REVERT: I 693 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7472 (mp) REVERT: I 731 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7491 (ptp90) REVERT: I 951 MET cc_start: 0.9107 (tmm) cc_final: 0.8763 (ppp) REVERT: I 958 LYS cc_start: 0.9332 (tmtt) cc_final: 0.8860 (tptp) REVERT: I 1023 HIS cc_start: 0.9230 (m90) cc_final: 0.9005 (m90) REVERT: I 1032 LYS cc_start: 0.9505 (mmtm) cc_final: 0.9302 (mmtm) REVERT: I 1034 ARG cc_start: 0.9455 (tpt90) cc_final: 0.9100 (tpt90) REVERT: I 1089 GLU cc_start: 0.8218 (tp30) cc_final: 0.7784 (tp30) REVERT: I 1127 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8068 (mttp) REVERT: I 1166 ASP cc_start: 0.8703 (m-30) cc_final: 0.7827 (t0) REVERT: I 1170 MET cc_start: 0.8313 (mmt) cc_final: 0.7874 (mmt) REVERT: I 1174 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8210 (tp30) REVERT: I 1176 LEU cc_start: 0.8827 (mp) cc_final: 0.8510 (mp) REVERT: I 1194 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: I 1230 MET cc_start: 0.8669 (ttp) cc_final: 0.8385 (ttt) REVERT: I 1240 ASP cc_start: 0.8522 (p0) cc_final: 0.8039 (t70) REVERT: I 1243 MET cc_start: 0.8687 (ttp) cc_final: 0.8452 (tmm) REVERT: I 1281 TYR cc_start: 0.8783 (m-80) cc_final: 0.8469 (m-10) REVERT: I 1290 MET cc_start: 0.8532 (tpp) cc_final: 0.8301 (tpp) REVERT: I 1327 LEU cc_start: 0.7868 (tt) cc_final: 0.7585 (pp) REVERT: J 37 GLU cc_start: 0.8014 (tp30) cc_final: 0.7803 (tp30) REVERT: J 189 LEU cc_start: 0.9437 (mp) cc_final: 0.9028 (pp) REVERT: J 198 CYS cc_start: 0.8700 (m) cc_final: 0.8121 (p) REVERT: J 339 ARG cc_start: 0.7285 (mmm-85) cc_final: 0.6964 (mmm-85) REVERT: J 340 GLN cc_start: 0.7819 (tp40) cc_final: 0.7564 (tp40) REVERT: J 372 MET cc_start: 0.8569 (mtp) cc_final: 0.8324 (mtp) REVERT: J 400 MET cc_start: 0.8004 (mmm) cc_final: 0.7072 (mmm) REVERT: J 417 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7752 (mmm-85) REVERT: J 449 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7459 (tp) REVERT: J 604 MET cc_start: 0.8225 (ttt) cc_final: 0.8020 (ttt) REVERT: J 644 MET cc_start: 0.7806 (ptp) cc_final: 0.7542 (ptp) REVERT: J 739 GLN cc_start: 0.8341 (pt0) cc_final: 0.8096 (pt0) REVERT: J 822 MET cc_start: 0.8110 (mmt) cc_final: 0.7874 (tpt) REVERT: J 844 THR cc_start: 0.8502 (p) cc_final: 0.8185 (t) REVERT: J 1003 LEU cc_start: 0.8167 (tp) cc_final: 0.7862 (tp) REVERT: J 1040 MET cc_start: 0.4791 (mtt) cc_final: 0.1799 (ppp) REVERT: J 1155 ILE cc_start: 0.9464 (mm) cc_final: 0.9189 (tp) REVERT: J 1189 MET cc_start: 0.7787 (ttm) cc_final: 0.7090 (tmm) REVERT: J 1260 MET cc_start: 0.7621 (mtt) cc_final: 0.7415 (tpp) REVERT: J 1281 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7548 (tm-30) REVERT: J 1284 ARG cc_start: 0.8857 (mmm160) cc_final: 0.8360 (mmm160) REVERT: J 1297 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8160 (pttm) REVERT: K 29 GLN cc_start: 0.9132 (mt0) cc_final: 0.8182 (tm-30) REVERT: K 30 MET cc_start: 0.7506 (mtt) cc_final: 0.6734 (mmt) REVERT: K 52 ARG cc_start: 0.8822 (mtp180) cc_final: 0.8203 (ptm160) REVERT: K 61 ASN cc_start: 0.8612 (m-40) cc_final: 0.8162 (t0) outliers start: 84 outliers final: 57 residues processed: 608 average time/residue: 0.1743 time to fit residues: 162.1200 Evaluate side-chains 545 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 482 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 75 GLN 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 46 ILE Chi-restraints excluded: chain H residue 50 SER 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 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 158 ASP Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 279 LYS Chi-restraints excluded: chain I residue 343 HIS Chi-restraints excluded: chain I residue 384 LEU Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 693 LEU 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 922 ASN Chi-restraints excluded: chain I residue 998 LEU Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER 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 352 ARG Chi-restraints excluded: chain J residue 408 VAL Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 470 VAL Chi-restraints excluded: chain J residue 478 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 694 SER Chi-restraints excluded: chain J residue 740 LEU 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 882 VAL Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1297 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 92 optimal weight: 0.8980 chunk 271 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 170 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 27 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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** I 133 ASN I 276 GLN ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 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 = 0.4524 r_free = 0.4524 target = 0.204886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.130570 restraints weight = 44374.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.136996 restraints weight = 25263.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137181 restraints weight = 14292.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.137237 restraints weight = 14128.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.137845 restraints weight = 14282.374| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 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 : 0.004 0.061 26089 Z= 0.187 Angle : 0.692 12.572 35444 Z= 0.351 Chirality : 0.044 0.285 4051 Planarity : 0.006 0.088 4467 Dihedral : 14.382 175.873 4033 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 3.77 % Allowed : 21.82 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3124 helix: 0.68 (0.16), residues: 1113 sheet: -0.81 (0.25), residues: 408 loop : -1.56 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 359 TYR 0.038 0.002 TYR H 177 PHE 0.018 0.002 PHE I 80 TRP 0.009 0.001 TRP I1276 HIS 0.007 0.001 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00437 (26081) covalent geometry : angle 0.68887 (35432) hydrogen bonds : bond 0.04081 ( 1046) hydrogen bonds : angle 5.00217 ( 2917) metal coordination : bond 0.00914 ( 8) metal coordination : angle 3.43211 ( 12) *********************** 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 610 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 509 time to evaluate : 0.748 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: G 10 LYS cc_start: 0.8338 (mmtm) cc_final: 0.7482 (mmtm) REVERT: G 51 MET cc_start: 0.8940 (mmm) cc_final: 0.8628 (mmm) REVERT: G 58 GLU cc_start: 0.7190 (tt0) cc_final: 0.6745 (tt0) REVERT: G 71 LYS cc_start: 0.8591 (tptt) cc_final: 0.8273 (tptm) REVERT: G 125 LYS cc_start: 0.8641 (tttt) cc_final: 0.7982 (tttm) REVERT: G 145 LYS cc_start: 0.8627 (ttmm) cc_final: 0.7941 (tptp) REVERT: G 181 GLU cc_start: 0.7376 (mp0) cc_final: 0.6641 (mp0) REVERT: G 206 GLU cc_start: 0.7182 (tp30) cc_final: 0.6549 (tp30) REVERT: G 227 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8972 (mm-40) REVERT: H 18 GLN cc_start: 0.8863 (pm20) cc_final: 0.8590 (mp10) REVERT: H 152 TYR cc_start: 0.7514 (t80) cc_final: 0.7177 (t80) REVERT: I 37 LYS cc_start: 0.8544 (ttpt) cc_final: 0.7941 (tptm) REVERT: I 97 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7116 (mmm-85) REVERT: I 121 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8366 (tm-30) REVERT: I 151 ARG cc_start: 0.8203 (ttt-90) cc_final: 0.8001 (mtp85) REVERT: I 207 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7628 (p) REVERT: I 213 LEU cc_start: 0.8159 (mm) cc_final: 0.7887 (mm) REVERT: I 315 MET cc_start: 0.8967 (tmm) cc_final: 0.8659 (tmm) REVERT: I 363 LEU cc_start: 0.9207 (mt) cc_final: 0.8957 (tp) REVERT: I 693 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7572 (mp) REVERT: I 731 ARG cc_start: 0.8105 (ptp90) cc_final: 0.7545 (ptp90) REVERT: I 865 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7755 (mt) REVERT: I 958 LYS cc_start: 0.9317 (tmtt) cc_final: 0.8874 (tptp) REVERT: I 1034 ARG cc_start: 0.9467 (tpt90) cc_final: 0.8990 (tpt90) REVERT: I 1089 GLU cc_start: 0.8259 (tp30) cc_final: 0.7935 (tp30) REVERT: I 1119 MET cc_start: 0.8084 (ttp) cc_final: 0.7864 (tpp) REVERT: I 1127 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8045 (mttp) REVERT: I 1166 ASP cc_start: 0.8553 (m-30) cc_final: 0.7730 (t0) REVERT: I 1170 MET cc_start: 0.8275 (mmt) cc_final: 0.7932 (mmt) REVERT: I 1174 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7918 (tp30) REVERT: I 1194 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: I 1230 MET cc_start: 0.8664 (ttp) cc_final: 0.8341 (ttt) REVERT: I 1240 ASP cc_start: 0.8606 (p0) cc_final: 0.8205 (t70) REVERT: I 1281 TYR cc_start: 0.8891 (m-80) cc_final: 0.8540 (m-10) REVERT: I 1304 MET cc_start: 0.7752 (ttm) cc_final: 0.7432 (ttm) REVERT: I 1327 LEU cc_start: 0.7905 (tt) cc_final: 0.7607 (pp) REVERT: J 37 GLU cc_start: 0.8045 (tp30) cc_final: 0.7825 (tp30) REVERT: J 115 TRP cc_start: 0.8196 (m-10) cc_final: 0.7860 (m-10) REVERT: J 189 LEU cc_start: 0.9438 (mp) cc_final: 0.9033 (pp) REVERT: J 341 ASN cc_start: 0.8625 (m110) cc_final: 0.7322 (t0) REVERT: J 400 MET cc_start: 0.7885 (mmm) cc_final: 0.7680 (mmm) REVERT: J 417 ARG cc_start: 0.8212 (tpt170) cc_final: 0.7882 (mmm160) REVERT: J 449 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7698 (tp) REVERT: J 821 MET cc_start: 0.8240 (tpp) cc_final: 0.7522 (tpp) REVERT: J 844 THR cc_start: 0.8671 (p) cc_final: 0.8413 (t) REVERT: J 891 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7577 (t0) REVERT: J 995 TYR cc_start: 0.8089 (m-80) cc_final: 0.7560 (m-10) REVERT: J 1003 LEU cc_start: 0.8229 (tp) cc_final: 0.7915 (tp) REVERT: J 1040 MET cc_start: 0.4850 (mtt) cc_final: 0.1810 (ppp) REVERT: J 1155 ILE cc_start: 0.9405 (mm) cc_final: 0.9132 (tp) REVERT: J 1189 MET cc_start: 0.7819 (ttm) cc_final: 0.7105 (tmm) REVERT: J 1297 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8162 (pttm) REVERT: J 1372 ARG cc_start: 0.6345 (mmp80) cc_final: 0.6116 (mmp80) REVERT: K 29 GLN cc_start: 0.9111 (mt0) cc_final: 0.8139 (tm-30) REVERT: K 30 MET cc_start: 0.7403 (mtt) cc_final: 0.6644 (mmt) REVERT: K 52 ARG cc_start: 0.8852 (mtp180) cc_final: 0.8196 (ptm160) REVERT: K 61 ASN cc_start: 0.8638 (m-40) cc_final: 0.8153 (t0) outliers start: 101 outliers final: 66 residues processed: 578 average time/residue: 0.1731 time to fit residues: 153.1717 Evaluate side-chains 550 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 477 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 81 ILE 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 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 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 144 VAL Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 700 VAL 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 998 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1207 SER 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 352 ARG 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 470 VAL Chi-restraints excluded: chain J residue 478 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 694 SER Chi-restraints excluded: chain J residue 728 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 760 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 1257 VAL Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1297 LYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 166 optimal weight: 0.0980 chunk 299 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 45 optimal weight: 0.1980 chunk 245 optimal weight: 0.0060 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 ** I 519 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 = 0.4560 r_free = 0.4560 target = 0.208742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155918 restraints weight = 44844.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154368 restraints weight = 31291.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155599 restraints weight = 28383.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.156290 restraints weight = 19154.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158524 restraints weight = 17027.842| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26089 Z= 0.128 Angle : 0.680 15.128 35444 Z= 0.341 Chirality : 0.043 0.275 4051 Planarity : 0.005 0.066 4467 Dihedral : 14.262 175.137 4032 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.72 % Rotamer: Outliers : 3.36 % Allowed : 23.27 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.15), residues: 3124 helix: 0.81 (0.16), residues: 1100 sheet: -0.55 (0.25), residues: 408 loop : -1.52 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 12 TYR 0.055 0.001 TYR H 177 PHE 0.014 0.001 PHE J1319 TRP 0.018 0.001 TRP I1276 HIS 0.010 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00294 (26081) covalent geometry : angle 0.67874 (35432) hydrogen bonds : bond 0.03798 ( 1046) hydrogen bonds : angle 4.83119 ( 2917) metal coordination : bond 0.00380 ( 8) metal coordination : angle 2.18737 ( 12) *********************** 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 610 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 520 time to evaluate : 1.100 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: G 51 MET cc_start: 0.8741 (mmm) cc_final: 0.8503 (mmm) REVERT: G 71 LYS cc_start: 0.8518 (tptt) cc_final: 0.8260 (tptm) REVERT: G 125 LYS cc_start: 0.8530 (tttt) cc_final: 0.8030 (tttm) REVERT: G 145 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8062 (tptp) REVERT: G 181 GLU cc_start: 0.7226 (mp0) cc_final: 0.6579 (mp0) REVERT: G 206 GLU cc_start: 0.7230 (tp30) cc_final: 0.6710 (tp30) REVERT: H 127 GLN cc_start: 0.9112 (pm20) cc_final: 0.8905 (pm20) REVERT: H 147 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8343 (tm-30) REVERT: H 152 TYR cc_start: 0.7124 (t80) cc_final: 0.6807 (t80) REVERT: H 200 LYS cc_start: 0.7962 (tttp) cc_final: 0.7743 (tptp) REVERT: H 208 ASN cc_start: 0.9283 (p0) cc_final: 0.9079 (p0) REVERT: I 37 LYS cc_start: 0.8448 (ttpt) cc_final: 0.7736 (tttm) REVERT: I 97 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.6990 (mmm-85) REVERT: I 213 LEU cc_start: 0.7691 (mm) cc_final: 0.7473 (mm) REVERT: I 369 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7811 (ppp) REVERT: I 429 MET cc_start: 0.7927 (mmt) cc_final: 0.7722 (mmt) REVERT: I 524 ILE cc_start: 0.9158 (tp) cc_final: 0.8903 (tp) REVERT: I 540 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8100 (ttm110) REVERT: I 575 LEU cc_start: 0.8282 (tp) cc_final: 0.7799 (mt) REVERT: I 653 MET cc_start: 0.7695 (tpp) cc_final: 0.6847 (tpt) REVERT: I 693 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7276 (mp) REVERT: I 731 ARG cc_start: 0.7905 (ptp90) cc_final: 0.7516 (ptp90) REVERT: I 865 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7505 (mt) REVERT: I 958 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8645 (tptp) REVERT: I 1089 GLU cc_start: 0.8198 (tp30) cc_final: 0.7748 (tp30) REVERT: I 1127 LYS cc_start: 0.8316 (mmmm) cc_final: 0.8015 (mttp) REVERT: I 1166 ASP cc_start: 0.8189 (m-30) cc_final: 0.7570 (t0) REVERT: I 1170 MET cc_start: 0.7944 (mmt) cc_final: 0.7708 (mmt) REVERT: I 1174 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7818 (tp30) REVERT: I 1177 ARG cc_start: 0.8125 (ptm-80) cc_final: 0.7900 (ptm160) REVERT: I 1194 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7655 (mt-10) REVERT: I 1230 MET cc_start: 0.8633 (ttp) cc_final: 0.8403 (ttt) REVERT: I 1240 ASP cc_start: 0.8547 (p0) cc_final: 0.8250 (t0) REVERT: I 1281 TYR cc_start: 0.8764 (m-80) cc_final: 0.8508 (m-10) REVERT: I 1304 MET cc_start: 0.7426 (ttm) cc_final: 0.7203 (ttm) REVERT: I 1327 LEU cc_start: 0.8004 (tt) cc_final: 0.7679 (pp) REVERT: J 115 TRP cc_start: 0.8068 (m100) cc_final: 0.7810 (m-10) REVERT: J 123 ARG cc_start: 0.6749 (mmm160) cc_final: 0.6259 (mmp80) REVERT: J 189 LEU cc_start: 0.9197 (mp) cc_final: 0.8854 (pp) REVERT: J 298 MET cc_start: 0.5591 (mmt) cc_final: 0.5363 (tmm) REVERT: J 330 MET cc_start: 0.6921 (tpp) cc_final: 0.6599 (tpp) REVERT: J 340 GLN cc_start: 0.7388 (tp40) cc_final: 0.7159 (tp40) REVERT: J 341 ASN cc_start: 0.8430 (m110) cc_final: 0.7316 (m-40) REVERT: J 342 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6881 (mt) REVERT: J 400 MET cc_start: 0.7670 (mmm) cc_final: 0.7421 (mmm) REVERT: J 417 ARG cc_start: 0.7982 (tpt170) cc_final: 0.7578 (mmm160) REVERT: J 449 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7159 (tp) REVERT: J 504 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6477 (mt0) REVERT: J 739 GLN cc_start: 0.8091 (pt0) cc_final: 0.7859 (pt0) REVERT: J 1003 LEU cc_start: 0.7983 (tp) cc_final: 0.7739 (tp) REVERT: J 1040 MET cc_start: 0.4036 (mtt) cc_final: 0.1264 (ppp) REVERT: J 1189 MET cc_start: 0.6943 (ttm) cc_final: 0.6583 (tmm) REVERT: J 1372 ARG cc_start: 0.6381 (mmp80) cc_final: 0.6131 (mmp80) REVERT: K 26 ARG cc_start: 0.8596 (tpm170) cc_final: 0.8348 (tpt90) REVERT: K 52 ARG cc_start: 0.8811 (mtp180) cc_final: 0.8463 (mtp180) REVERT: K 61 ASN cc_start: 0.8246 (m-40) cc_final: 0.7886 (t0) REVERT: K 70 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8609 (pp30) outliers start: 90 outliers final: 67 residues processed: 576 average time/residue: 0.1698 time to fit residues: 149.3475 Evaluate side-chains 552 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 478 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 131 CYS 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 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 224 PHE Chi-restraints excluded: chain I residue 369 MET Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 498 ILE 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 663 VAL Chi-restraints excluded: chain I residue 693 LEU Chi-restraints excluded: chain I residue 700 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 922 ASN 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 1244 HIS 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 253 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 352 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 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 573 THR Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 728 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 769 VAL 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 960 LEU Chi-restraints excluded: chain J residue 977 SER Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 210 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 296 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 315 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 151 optimal weight: 0.0980 chunk 218 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1090 ASN J 274 ASN ** J 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.208537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135706 restraints weight = 44699.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.140413 restraints weight = 22577.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143355 restraints weight = 15203.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145112 restraints weight = 12375.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145786 restraints weight = 11159.500| |-----------------------------------------------------------------------------| r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26089 Z= 0.132 Angle : 0.689 16.264 35444 Z= 0.343 Chirality : 0.043 0.257 4051 Planarity : 0.005 0.063 4467 Dihedral : 14.224 174.379 4030 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.19 % Favored : 94.78 % Rotamer: Outliers : 3.32 % Allowed : 23.61 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.15), residues: 3124 helix: 0.76 (0.16), residues: 1107 sheet: -0.53 (0.26), residues: 397 loop : -1.48 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I1033 TYR 0.034 0.001 TYR H 177 PHE 0.020 0.001 PHE I 80 TRP 0.019 0.002 TRP I1276 HIS 0.007 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00305 (26081) covalent geometry : angle 0.68797 (35432) hydrogen bonds : bond 0.03704 ( 1046) hydrogen bonds : angle 4.81722 ( 2917) metal coordination : bond 0.00438 ( 8) metal coordination : angle 1.87193 ( 12) *********************** 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 578 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 489 time to evaluate : 0.965 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 33 ARG cc_start: 0.7508 (tpp80) cc_final: 0.7112 (mmt-90) REVERT: G 51 MET cc_start: 0.8829 (mmm) cc_final: 0.8539 (mmm) REVERT: G 71 LYS cc_start: 0.8562 (tptt) cc_final: 0.8330 (tptm) REVERT: G 125 LYS cc_start: 0.8621 (tttt) cc_final: 0.8106 (tttm) REVERT: G 145 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8022 (tptp) REVERT: G 181 GLU cc_start: 0.7202 (mp0) cc_final: 0.6539 (mp0) REVERT: G 206 GLU cc_start: 0.7250 (tp30) cc_final: 0.6694 (tp30) REVERT: H 147 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8459 (tm-30) REVERT: H 152 TYR cc_start: 0.7219 (t80) cc_final: 0.6757 (t80) REVERT: H 208 ASN cc_start: 0.9321 (p0) cc_final: 0.9106 (p0) REVERT: I 37 LYS cc_start: 0.8452 (ttpt) cc_final: 0.7880 (tttm) REVERT: I 213 LEU cc_start: 0.7798 (mm) cc_final: 0.7563 (mm) REVERT: I 524 ILE cc_start: 0.9293 (tp) cc_final: 0.9059 (tp) REVERT: I 575 LEU cc_start: 0.8681 (tp) cc_final: 0.8142 (mt) REVERT: I 653 MET cc_start: 0.7770 (tpp) cc_final: 0.7170 (tpt) REVERT: I 731 ARG cc_start: 0.8023 (ptp90) cc_final: 0.7542 (ptp90) REVERT: I 865 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7534 (mt) REVERT: I 958 LYS cc_start: 0.9228 (tmtt) cc_final: 0.8761 (tptp) REVERT: I 1089 GLU cc_start: 0.8148 (tp30) cc_final: 0.7749 (tp30) REVERT: I 1127 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7963 (mttp) REVERT: I 1166 ASP cc_start: 0.8010 (m-30) cc_final: 0.7520 (t0) REVERT: I 1174 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7882 (tp30) REVERT: I 1194 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: I 1230 MET cc_start: 0.8648 (ttp) cc_final: 0.8333 (ttt) REVERT: I 1240 ASP cc_start: 0.8466 (p0) cc_final: 0.8189 (t0) REVERT: I 1281 TYR cc_start: 0.8812 (m-80) cc_final: 0.8560 (m-10) REVERT: I 1304 MET cc_start: 0.7326 (ttm) cc_final: 0.7102 (ttm) REVERT: I 1332 SER cc_start: 0.6976 (OUTLIER) cc_final: 0.6765 (p) REVERT: J 115 TRP cc_start: 0.8041 (m100) cc_final: 0.7705 (m-10) REVERT: J 123 ARG cc_start: 0.7229 (mmm160) cc_final: 0.6659 (mmp80) REVERT: J 189 LEU cc_start: 0.9422 (mp) cc_final: 0.9025 (pp) REVERT: J 298 MET cc_start: 0.5354 (mmt) cc_final: 0.5093 (tmm) REVERT: J 341 ASN cc_start: 0.8138 (m110) cc_final: 0.7051 (t0) REVERT: J 342 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7170 (mt) REVERT: J 400 MET cc_start: 0.7593 (mmm) cc_final: 0.7389 (mmm) REVERT: J 404 GLU cc_start: 0.7535 (tp30) cc_final: 0.7328 (tp30) REVERT: J 417 ARG cc_start: 0.7914 (tpt170) cc_final: 0.7601 (mmm160) REVERT: J 449 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7414 (tp) REVERT: J 490 ILE cc_start: 0.9262 (pt) cc_final: 0.8784 (mt) REVERT: J 504 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6391 (mt0) REVERT: J 891 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7244 (t0) REVERT: J 1003 LEU cc_start: 0.8267 (tp) cc_final: 0.8004 (tp) REVERT: J 1040 MET cc_start: 0.4889 (mtt) cc_final: 0.1914 (ppp) REVERT: J 1189 MET cc_start: 0.7368 (ttm) cc_final: 0.6752 (tmm) REVERT: K 26 ARG cc_start: 0.8693 (tpm170) cc_final: 0.8225 (tpm170) REVERT: K 52 ARG cc_start: 0.8765 (mtp180) cc_final: 0.8430 (mtp180) REVERT: K 61 ASN cc_start: 0.8301 (m-40) cc_final: 0.7914 (t0) outliers start: 89 outliers final: 71 residues processed: 547 average time/residue: 0.1657 time to fit residues: 139.4336 Evaluate side-chains 549 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 471 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 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 180 VAL Chi-restraints excluded: chain H residue 183 ILE 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 224 PHE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE 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 700 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 1094 VAL Chi-restraints excluded: chain I residue 1194 GLU 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 253 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 352 ARG Chi-restraints excluded: chain J residue 374 LEU 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 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 506 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 694 SER Chi-restraints excluded: chain J residue 728 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 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 1209 VAL Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 25 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 249 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 272 optimal weight: 40.0000 chunk 171 optimal weight: 5.9990 chunk 180 optimal weight: 0.0970 chunk 163 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 23 HIS ** 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 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.207077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134048 restraints weight = 44544.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139815 restraints weight = 24589.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.140639 restraints weight = 15197.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.141202 restraints weight = 13754.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.141665 restraints weight = 13774.345| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26089 Z= 0.160 Angle : 0.704 13.383 35444 Z= 0.351 Chirality : 0.044 0.256 4051 Planarity : 0.005 0.064 4467 Dihedral : 14.221 174.296 4030 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 3.77 % Allowed : 23.65 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.15), residues: 3124 helix: 0.73 (0.16), residues: 1112 sheet: -0.55 (0.26), residues: 401 loop : -1.46 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I1033 TYR 0.022 0.001 TYR H 177 PHE 0.015 0.001 PHE I 506 TRP 0.023 0.001 TRP I1276 HIS 0.004 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00377 (26081) covalent geometry : angle 0.70361 (35432) hydrogen bonds : bond 0.03763 ( 1046) hydrogen bonds : angle 4.79649 ( 2917) metal coordination : bond 0.00678 ( 8) metal coordination : angle 1.85199 ( 12) *********************** 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 587 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 486 time to evaluate : 0.818 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: G 33 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7416 (mmt-90) REVERT: G 51 MET cc_start: 0.8830 (mmm) cc_final: 0.8621 (mmm) REVERT: G 58 GLU cc_start: 0.7802 (tt0) cc_final: 0.7547 (tt0) REVERT: G 71 LYS cc_start: 0.8593 (tptt) cc_final: 0.8349 (tptm) REVERT: G 125 LYS cc_start: 0.8705 (tttt) cc_final: 0.8150 (tttm) REVERT: G 145 LYS cc_start: 0.8643 (ttmm) cc_final: 0.7906 (tptp) REVERT: H 18 GLN cc_start: 0.8661 (mp10) cc_final: 0.8370 (mp10) REVERT: H 200 LYS cc_start: 0.8025 (tttp) cc_final: 0.7790 (tptt) REVERT: I 37 LYS cc_start: 0.8524 (ttpt) cc_final: 0.7839 (tttm) REVERT: I 213 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7697 (mm) REVERT: I 431 LYS cc_start: 0.8748 (tppt) cc_final: 0.8484 (tppt) REVERT: I 524 ILE cc_start: 0.9333 (tp) cc_final: 0.9099 (tp) REVERT: I 653 MET cc_start: 0.7835 (tpp) cc_final: 0.7156 (tpt) REVERT: I 731 ARG cc_start: 0.8075 (ptp90) cc_final: 0.7560 (ptp90) REVERT: I 865 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7546 (mt) REVERT: I 958 LYS cc_start: 0.9255 (tmtt) cc_final: 0.8751 (tptp) REVERT: I 1034 ARG cc_start: 0.9324 (tpt90) cc_final: 0.8819 (tpt90) REVERT: I 1064 ASP cc_start: 0.7423 (t70) cc_final: 0.7025 (t70) REVERT: I 1089 GLU cc_start: 0.8184 (tp30) cc_final: 0.7770 (tp30) REVERT: I 1119 MET cc_start: 0.8022 (tpp) cc_final: 0.7571 (ttp) REVERT: I 1127 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7984 (mttp) REVERT: I 1166 ASP cc_start: 0.8478 (m-30) cc_final: 0.7915 (t0) REVERT: I 1170 MET cc_start: 0.8265 (mmt) cc_final: 0.7849 (mmt) REVERT: I 1174 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8028 (tp30) REVERT: I 1194 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: I 1230 MET cc_start: 0.8680 (ttp) cc_final: 0.8407 (ttt) REVERT: I 1240 ASP cc_start: 0.8551 (p0) cc_final: 0.8300 (t0) REVERT: I 1281 TYR cc_start: 0.8911 (m-80) cc_final: 0.8658 (m-10) REVERT: I 1295 SER cc_start: 0.9048 (p) cc_final: 0.8787 (p) REVERT: I 1304 MET cc_start: 0.7588 (ttm) cc_final: 0.7244 (ttm) REVERT: I 1327 LEU cc_start: 0.7886 (tt) cc_final: 0.7566 (pp) REVERT: J 37 GLU cc_start: 0.7960 (tp30) cc_final: 0.7636 (tp30) REVERT: J 115 TRP cc_start: 0.8015 (m100) cc_final: 0.7703 (m-10) REVERT: J 123 ARG cc_start: 0.7266 (mmm160) cc_final: 0.6716 (mmp80) REVERT: J 189 LEU cc_start: 0.9405 (mp) cc_final: 0.9006 (pp) REVERT: J 298 MET cc_start: 0.5599 (mmt) cc_final: 0.5292 (tmm) REVERT: J 340 GLN cc_start: 0.7562 (tp40) cc_final: 0.7351 (tp40) REVERT: J 341 ASN cc_start: 0.8314 (m110) cc_final: 0.7170 (m-40) REVERT: J 342 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7100 (mt) REVERT: J 417 ARG cc_start: 0.8014 (tpt170) cc_final: 0.7609 (mmm160) REVERT: J 428 THR cc_start: 0.8551 (m) cc_final: 0.8305 (m) REVERT: J 449 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7354 (tp) REVERT: J 504 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6128 (pt0) REVERT: J 646 ILE cc_start: 0.8346 (mm) cc_final: 0.7594 (tp) REVERT: J 821 MET cc_start: 0.8367 (mmm) cc_final: 0.8019 (tpp) REVERT: J 891 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7232 (t0) REVERT: J 1003 LEU cc_start: 0.8272 (tp) cc_final: 0.7987 (tp) REVERT: J 1040 MET cc_start: 0.4958 (mtt) cc_final: 0.2150 (ppp) REVERT: J 1189 MET cc_start: 0.7668 (ttm) cc_final: 0.6959 (tmm) REVERT: J 1262 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.8037 (ttp-110) REVERT: J 1372 ARG cc_start: 0.6167 (mmp80) cc_final: 0.5967 (mmp80) REVERT: K 29 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8662 (pp30) REVERT: K 52 ARG cc_start: 0.8846 (mtp180) cc_final: 0.8360 (mtp180) outliers start: 101 outliers final: 79 residues processed: 555 average time/residue: 0.1506 time to fit residues: 128.3676 Evaluate side-chains 554 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 466 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 178 SER Chi-restraints excluded: chain H residue 46 ILE 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 198 LEU Chi-restraints excluded: chain I residue 6 THR 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 213 LEU Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL 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 623 LEU 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 727 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 922 ASN Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1194 GLU 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 374 LEU 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 470 VAL Chi-restraints excluded: chain J residue 478 LEU Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 506 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 694 SER Chi-restraints excluded: chain J residue 728 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 769 VAL 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 1209 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1262 ARG Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 29 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 250 optimal weight: 0.6980 chunk 284 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 246 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 270 optimal weight: 0.0670 chunk 50 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 23 HIS ** 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 519 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** ** J1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.209068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136371 restraints weight = 44680.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.141008 restraints weight = 22482.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143971 restraints weight = 15191.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.145638 restraints weight = 12400.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146154 restraints weight = 11213.128| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26089 Z= 0.133 Angle : 0.715 14.098 35444 Z= 0.354 Chirality : 0.044 0.250 4051 Planarity : 0.005 0.064 4467 Dihedral : 14.199 174.372 4030 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 3.25 % Allowed : 24.21 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.15), residues: 3124 helix: 0.73 (0.16), residues: 1096 sheet: -0.51 (0.26), residues: 402 loop : -1.44 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 540 TYR 0.023 0.001 TYR H 177 PHE 0.022 0.001 PHE I 80 TRP 0.021 0.001 TRP I1276 HIS 0.004 0.001 HIS I1023 Details of bonding type rmsd covalent geometry : bond 0.00313 (26081) covalent geometry : angle 0.71435 (35432) hydrogen bonds : bond 0.03664 ( 1046) hydrogen bonds : angle 4.76578 ( 2917) metal coordination : bond 0.00428 ( 8) metal coordination : angle 1.75668 ( 12) *********************** 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 575 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 488 time to evaluate : 0.826 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 51 MET cc_start: 0.8814 (mmm) cc_final: 0.8582 (mmm) REVERT: G 71 LYS cc_start: 0.8581 (tptt) cc_final: 0.8362 (tptm) REVERT: G 125 LYS cc_start: 0.8666 (tttt) cc_final: 0.8233 (tttm) REVERT: G 145 LYS cc_start: 0.8587 (ttmm) cc_final: 0.7896 (tptp) REVERT: G 227 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8931 (mm-40) REVERT: H 18 GLN cc_start: 0.8614 (mp10) cc_final: 0.8289 (mp10) REVERT: H 186 ASN cc_start: 0.8074 (t0) cc_final: 0.7692 (m-40) REVERT: H 200 LYS cc_start: 0.7942 (tttp) cc_final: 0.7735 (tmmt) REVERT: I 37 LYS cc_start: 0.8327 (ttpt) cc_final: 0.7578 (tttm) REVERT: I 213 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7582 (mm) REVERT: I 431 LYS cc_start: 0.8688 (tppt) cc_final: 0.8404 (tppt) REVERT: I 524 ILE cc_start: 0.9295 (tp) cc_final: 0.9071 (tp) REVERT: I 653 MET cc_start: 0.7686 (tpp) cc_final: 0.7065 (tpt) REVERT: I 731 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7536 (ptp90) REVERT: I 790 ASP cc_start: 0.8468 (p0) cc_final: 0.8191 (p0) REVERT: I 865 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7395 (mt) REVERT: I 958 LYS cc_start: 0.9238 (tmtt) cc_final: 0.8739 (tptp) REVERT: I 1034 ARG cc_start: 0.9258 (tpt90) cc_final: 0.8811 (tpt90) REVERT: I 1064 ASP cc_start: 0.7366 (t70) cc_final: 0.7023 (t70) REVERT: I 1089 GLU cc_start: 0.8147 (tp30) cc_final: 0.7729 (tp30) REVERT: I 1127 LYS cc_start: 0.8203 (mmmm) cc_final: 0.7941 (mttp) REVERT: I 1166 ASP cc_start: 0.8138 (m-30) cc_final: 0.7727 (t0) REVERT: I 1170 MET cc_start: 0.7879 (mmt) cc_final: 0.7526 (mmt) REVERT: I 1174 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8093 (tp30) REVERT: I 1176 LEU cc_start: 0.8790 (mp) cc_final: 0.8547 (mp) REVERT: I 1194 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: I 1230 MET cc_start: 0.8671 (ttp) cc_final: 0.8368 (ttt) REVERT: I 1281 TYR cc_start: 0.8822 (m-80) cc_final: 0.8547 (m-10) REVERT: I 1295 SER cc_start: 0.9006 (p) cc_final: 0.8735 (p) REVERT: I 1327 LEU cc_start: 0.7906 (tt) cc_final: 0.7572 (pp) REVERT: J 37 GLU cc_start: 0.7979 (tp30) cc_final: 0.7672 (tp30) REVERT: J 115 TRP cc_start: 0.7984 (m100) cc_final: 0.7673 (m-10) REVERT: J 189 LEU cc_start: 0.9433 (mp) cc_final: 0.9038 (pp) REVERT: J 339 ARG cc_start: 0.7284 (mmm-85) cc_final: 0.6860 (mmm-85) REVERT: J 341 ASN cc_start: 0.8164 (m110) cc_final: 0.7163 (t0) REVERT: J 342 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7023 (mt) REVERT: J 417 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7573 (mmm160) REVERT: J 449 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7360 (tp) REVERT: J 475 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8312 (mm-30) REVERT: J 504 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6426 (mt0) REVERT: J 604 MET cc_start: 0.7814 (ttt) cc_final: 0.7594 (ttt) REVERT: J 646 ILE cc_start: 0.8037 (mm) cc_final: 0.7218 (tp) REVERT: J 739 GLN cc_start: 0.8309 (pt0) cc_final: 0.7998 (tt0) REVERT: J 821 MET cc_start: 0.8188 (mmm) cc_final: 0.7985 (tpp) REVERT: J 891 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7166 (t0) REVERT: J 1003 LEU cc_start: 0.8318 (tp) cc_final: 0.8070 (tp) REVERT: J 1040 MET cc_start: 0.5120 (mtt) cc_final: 0.2294 (ppp) REVERT: J 1189 MET cc_start: 0.7503 (ttm) cc_final: 0.6868 (tmm) REVERT: J 1372 ARG cc_start: 0.6529 (mmp80) cc_final: 0.6275 (mmp80) REVERT: K 52 ARG cc_start: 0.8662 (mtp180) cc_final: 0.8229 (mtp180) outliers start: 87 outliers final: 75 residues processed: 547 average time/residue: 0.1552 time to fit residues: 130.3833 Evaluate side-chains 541 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 459 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 213 LEU Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL 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 700 VAL Chi-restraints excluded: chain I residue 727 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 922 ASN 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 1244 HIS 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 237 MET 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 429 LEU 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 504 GLN Chi-restraints excluded: chain J residue 506 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 694 SER Chi-restraints excluded: chain J residue 728 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 769 VAL Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 810 THR Chi-restraints excluded: chain J residue 874 GLU 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 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 29 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 73 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 230 optimal weight: 3.9990 chunk 297 optimal weight: 0.8980 chunk 220 optimal weight: 0.4980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 23 HIS ** 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 147 GLN H 227 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 658 GLN I1129 ASN ** I1288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 157 GLN ** 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** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.206634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133827 restraints weight = 44574.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139176 restraints weight = 23400.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141529 restraints weight = 14287.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141311 restraints weight = 12880.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141484 restraints weight = 12727.858| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26089 Z= 0.177 Angle : 0.740 13.504 35444 Z= 0.369 Chirality : 0.045 0.249 4051 Planarity : 0.005 0.074 4467 Dihedral : 14.217 174.316 4030 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 3.44 % Allowed : 24.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.15), residues: 3124 helix: 0.67 (0.16), residues: 1097 sheet: -0.59 (0.26), residues: 403 loop : -1.44 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 388 TYR 0.023 0.002 TYR H 177 PHE 0.021 0.001 PHE J1319 TRP 0.023 0.002 TRP I1276 HIS 0.004 0.001 HIS I 551 Details of bonding type rmsd covalent geometry : bond 0.00419 (26081) covalent geometry : angle 0.73946 (35432) hydrogen bonds : bond 0.03846 ( 1046) hydrogen bonds : angle 4.84344 ( 2917) metal coordination : bond 0.00754 ( 8) metal coordination : angle 2.01558 ( 12) ********************** 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 557 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 465 time to evaluate : 0.829 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 71 LYS cc_start: 0.8620 (tptt) cc_final: 0.8399 (tptm) REVERT: G 125 LYS cc_start: 0.8721 (tttt) cc_final: 0.8281 (tttm) REVERT: G 170 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7412 (ptt180) REVERT: G 227 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8917 (mm-40) REVERT: H 18 GLN cc_start: 0.8637 (mp10) cc_final: 0.8314 (mp10) REVERT: I 37 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7610 (tttm) REVERT: I 431 LYS cc_start: 0.8728 (tppt) cc_final: 0.8428 (tppt) REVERT: I 654 ASP cc_start: 0.7203 (m-30) cc_final: 0.6934 (t0) REVERT: I 731 ARG cc_start: 0.8126 (ptp90) cc_final: 0.7556 (ptp90) REVERT: I 865 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7504 (mt) REVERT: I 958 LYS cc_start: 0.9261 (tmtt) cc_final: 0.8761 (tptp) REVERT: I 1034 ARG cc_start: 0.9291 (tpt90) cc_final: 0.8820 (tpt90) REVERT: I 1064 ASP cc_start: 0.7390 (t70) cc_final: 0.7043 (t70) REVERT: I 1089 GLU cc_start: 0.8181 (tp30) cc_final: 0.7763 (tp30) REVERT: I 1166 ASP cc_start: 0.8460 (m-30) cc_final: 0.7840 (t0) REVERT: I 1170 MET cc_start: 0.8208 (mmt) cc_final: 0.7833 (mmt) REVERT: I 1174 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7977 (tp30) REVERT: I 1176 LEU cc_start: 0.8705 (mp) cc_final: 0.8461 (mp) REVERT: I 1194 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7574 (mt-10) REVERT: I 1230 MET cc_start: 0.8636 (ttp) cc_final: 0.8317 (ttt) REVERT: I 1281 TYR cc_start: 0.8879 (m-80) cc_final: 0.8626 (m-10) REVERT: I 1327 LEU cc_start: 0.7858 (tt) cc_final: 0.7555 (pp) REVERT: J 31 ARG cc_start: 0.9411 (mtp180) cc_final: 0.9091 (mmm-85) REVERT: J 37 GLU cc_start: 0.7976 (tp30) cc_final: 0.7648 (tp30) REVERT: J 115 TRP cc_start: 0.8051 (m100) cc_final: 0.7746 (m-10) REVERT: J 130 MET cc_start: 0.6871 (ptm) cc_final: 0.6642 (ptp) REVERT: J 189 LEU cc_start: 0.9412 (mp) cc_final: 0.9017 (pp) REVERT: J 237 MET cc_start: 0.6866 (mmp) cc_final: 0.6545 (tpp) REVERT: J 341 ASN cc_start: 0.8531 (m110) cc_final: 0.7423 (m-40) REVERT: J 342 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7024 (mt) REVERT: J 417 ARG cc_start: 0.8015 (tpt170) cc_final: 0.7650 (mmm160) REVERT: J 449 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7657 (tp) REVERT: J 475 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8410 (mm-30) REVERT: J 504 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.6871 (mt0) REVERT: J 646 ILE cc_start: 0.8197 (mm) cc_final: 0.7702 (tp) REVERT: J 697 MET cc_start: 0.8374 (tmm) cc_final: 0.7714 (tmm) REVERT: J 821 MET cc_start: 0.8437 (mmm) cc_final: 0.7806 (tpp) REVERT: J 891 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7294 (t0) REVERT: J 1003 LEU cc_start: 0.8271 (tp) cc_final: 0.8018 (tp) REVERT: J 1040 MET cc_start: 0.4948 (mtt) cc_final: 0.2156 (ppp) REVERT: J 1189 MET cc_start: 0.7545 (ttm) cc_final: 0.6835 (tmm) REVERT: J 1281 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7355 (tm-30) REVERT: J 1297 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7780 (pttm) REVERT: J 1372 ARG cc_start: 0.6597 (mmp80) cc_final: 0.6354 (mmp80) REVERT: K 52 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8224 (mtp180) outliers start: 92 outliers final: 75 residues processed: 524 average time/residue: 0.1665 time to fit residues: 133.0865 Evaluate side-chains 536 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 454 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 46 ILE 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 147 GLN Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 198 LEU 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 169 LYS Chi-restraints excluded: chain I residue 224 PHE Chi-restraints excluded: chain I residue 336 LEU Chi-restraints excluded: chain I residue 370 MET Chi-restraints excluded: chain I residue 419 ILE Chi-restraints excluded: chain I residue 422 LYS Chi-restraints excluded: chain I residue 469 VAL 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 700 VAL Chi-restraints excluded: chain I residue 727 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 922 ASN Chi-restraints excluded: chain I residue 1094 VAL Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1194 GLU Chi-restraints excluded: chain I residue 1204 LEU 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 145 VAL Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 352 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 478 LEU Chi-restraints excluded: chain J residue 483 LEU Chi-restraints excluded: chain J residue 504 GLN Chi-restraints excluded: chain J residue 506 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 728 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 874 GLU 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 1209 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1297 LYS Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain J residue 1366 HIS Chi-restraints excluded: chain K residue 21 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 166 optimal weight: 0.4980 chunk 177 optimal weight: 0.2980 chunk 19 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 294 optimal weight: 0.9990 chunk 203 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 90 optimal weight: 0.0670 chunk 209 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.5722 ------------------------------------------------------------------------------- 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 23 HIS ** 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 147 GLN ** I 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1288 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** ** J1366 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 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 = 0.4543 r_free = 0.4543 target = 0.206969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.134195 restraints weight = 44423.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138921 restraints weight = 25106.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139759 restraints weight = 16674.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140443 restraints weight = 14053.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.141167 restraints weight = 14121.576| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.222 26089 Z= 0.208 Angle : 0.859 59.199 35444 Z= 0.453 Chirality : 0.048 1.084 4051 Planarity : 0.005 0.068 4467 Dihedral : 14.217 174.318 4030 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 3.29 % Allowed : 25.03 % Favored : 71.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.15), residues: 3124 helix: 0.68 (0.16), residues: 1096 sheet: -0.59 (0.26), residues: 403 loop : -1.43 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.078 0.001 ARG I 540 TYR 0.026 0.002 TYR I 291 PHE 0.018 0.001 PHE I 253 TRP 0.022 0.002 TRP I1276 HIS 0.007 0.001 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.00484 (26081) covalent geometry : angle 0.85798 (35432) hydrogen bonds : bond 0.03916 ( 1046) hydrogen bonds : angle 4.86408 ( 2917) metal coordination : bond 0.00578 ( 8) metal coordination : angle 1.99985 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5010.12 seconds wall clock time: 87 minutes 3.61 seconds (5223.61 seconds total)