Starting phenix.real_space_refine on Wed Mar 20 14:12:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rin_4892/03_2024/6rin_4892.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rin_4892/03_2024/6rin_4892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rin_4892/03_2024/6rin_4892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rin_4892/03_2024/6rin_4892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rin_4892/03_2024/6rin_4892.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rin_4892/03_2024/6rin_4892.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.074 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 58 5.49 5 Mg 1 5.21 5 S 110 5.16 5 C 17102 2.51 5 N 4878 2.21 5 O 5433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 42": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27584 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 392 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain breaks: 1 Chain: "T" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 550 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "F" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1292 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1772 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 219} Chain: "C" Number of atoms: 10407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1319, 10407 Classifications: {'peptide': 1319} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1263} Chain breaks: 1 Chain: "D" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "R" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 273 Classifications: {'RNA': 13} Modifications used: {'5*END': 1, 'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16630 SG CYS D 70 25.909 113.557 81.696 1.00128.74 S ATOM 16644 SG CYS D 72 24.797 116.651 82.496 1.00136.84 S ATOM 16752 SG CYS D 85 23.214 115.722 79.449 1.00118.16 S ATOM 16776 SG CYS D 88 26.754 115.071 78.842 1.00125.83 S ATOM 22464 SG CYS D 814 39.097 46.502 76.882 1.00 84.54 S ATOM 23029 SG CYS D 888 40.073 50.366 75.923 1.00 80.97 S ATOM 23080 SG CYS D 895 39.924 48.992 79.099 1.00 61.94 S ATOM 23101 SG CYS D 898 42.377 47.050 78.005 1.00 59.82 S Time building chain proxies: 13.96, per 1000 atoms: 0.51 Number of scatterers: 27584 At special positions: 0 Unit cell: (136.4, 151.8, 166.1, 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 110 16.00 P 58 15.00 Mg 1 11.99 O 5433 8.00 N 4878 7.00 C 17102 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 - 3.50 Amino acid : False - 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: 10.74 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " Number of angles added : 12 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6210 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 54 sheets defined 38.6% alpha, 13.4% beta 23 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 10.04 Creating SS restraints... Processing helix chain 'F' and resid 7 through 25 removed outlier: 3.702A pdb=" N GLU F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 38 removed outlier: 3.704A pdb=" N VAL F 29 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER F 38 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 71 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.985A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.617A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 233 removed outlier: 4.150A pdb=" N ASP A 233 " --> pdb=" O ALA A 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 154 through 161 removed outlier: 4.035A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.603A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.124A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.879A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.645A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.536A pdb=" N ARG C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 386 Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 480 Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 4.033A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 608 through 614 Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.127A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 666 removed outlier: 3.545A pdb=" N SER C 666 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.513A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.589A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 688 " --> pdb=" O ASN C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.971A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 826 removed outlier: 4.086A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 826 " --> pdb=" O VAL C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 865 removed outlier: 3.721A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 865 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 980 removed outlier: 3.884A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 990 removed outlier: 4.257A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.840A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.638A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.152A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.852A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.084A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.886A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1160 through 1164' Processing helix chain 'C' and resid 1167 through 1177 Processing helix chain 'C' and resid 1185 through 1189 removed outlier: 3.766A pdb=" N ASP C1188 " --> pdb=" O PRO C1185 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY C1189 " --> pdb=" O VAL C1186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1185 through 1189' Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.533A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1297 through 1309 Processing helix chain 'C' and resid 1321 through 1332 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.607A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.574A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 286 removed outlier: 4.292A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.721A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.780A pdb=" N ALA D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 removed outlier: 4.310A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 454 removed outlier: 3.739A pdb=" N VAL D 453 " --> pdb=" O HIS D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 removed outlier: 3.961A pdb=" N MET D 485 " --> pdb=" O ARG D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 489 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.776A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 613 removed outlier: 3.939A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.909A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.348A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 802 removed outlier: 3.765A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 874 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 940 through 946 removed outlier: 3.600A pdb=" N ALA D 945 " --> pdb=" O ALA D 941 " (cutoff:3.500A) Processing helix chain 'D' and resid 1051 through 1055 removed outlier: 3.739A pdb=" N THR D1054 " --> pdb=" O ASP D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 4.083A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1295 removed outlier: 3.666A pdb=" N ASN D1295 " --> pdb=" O GLU D1291 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1347 through 1354 Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.006A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.625A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 73 Processing sheet with id=AA1, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.683A pdb=" N TRP F 90 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE F 153 " --> pdb=" O TRP F 90 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU F 92 " --> pdb=" O ASN F 151 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 137 " --> pdb=" O TRP F 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 12 through 17 removed outlier: 5.184A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 24 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 97 through 104 removed outlier: 7.613A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA7, first strand: chain 'A' and resid 108 through 111 removed outlier: 4.007A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 133 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 removed outlier: 3.762A pdb=" N TYR A 177 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 13 through 18 removed outlier: 6.452A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 101 removed outlier: 6.906A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AB3, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AB4, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB5, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.323A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.048A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 59 through 60 removed outlier: 7.048A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 453 removed outlier: 6.558A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AC2, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC3, first strand: chain 'C' and resid 227 through 230 removed outlier: 3.633A pdb=" N VAL C 228 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.459A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.808A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.808A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 623 through 624 removed outlier: 4.411A pdb=" N HIS C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 716 through 717 removed outlier: 3.787A pdb=" N ALA C 784 " --> pdb=" O ALA C 716 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.006A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.731A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AD3, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.717A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 818 through 819 removed outlier: 7.318A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.580A pdb=" N ARG C1058 " --> pdb=" O THR C 830 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 835 through 839 Processing sheet with id=AD7, first strand: chain 'C' and resid 842 through 843 removed outlier: 3.820A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.587A pdb=" N VAL C 884 " --> pdb=" O LEU C 918 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AE1, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AE2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 4.046A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AE4, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.035A pdb=" N GLY D 36 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLU D 106 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.848A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AE7, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.436A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.382A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 706 through 707 removed outlier: 3.739A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AF2, first strand: chain 'D' and resid 825 through 826 removed outlier: 7.199A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 848 through 849 removed outlier: 6.719A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 991 through 995 removed outlier: 4.230A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.988A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.562A pdb=" N GLY D1033 " --> pdb=" O ILE D1115 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 1046 through 1047 Processing sheet with id=AF8, first strand: chain 'D' and resid 1162 through 1164 Processing sheet with id=AF9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.914A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 2877 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 13.54 Time building geometry restraints manager: 11.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7233 1.33 - 1.45: 4756 1.45 - 1.57: 15831 1.57 - 1.69: 113 1.69 - 1.81: 191 Bond restraints: 28124 Sorted by residual: bond pdb=" C SER A 178 " pdb=" N PRO A 179 " ideal model delta sigma weight residual 1.334 1.277 0.057 8.40e-03 1.42e+04 4.60e+01 bond pdb=" CA LEU C 448 " pdb=" C LEU C 448 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.34e-02 5.57e+03 3.08e+01 bond pdb=" C MET C1085 " pdb=" N PRO C1086 " ideal model delta sigma weight residual 1.332 1.281 0.051 1.12e-02 7.97e+03 2.07e+01 bond pdb=" CA CYS D 454 " pdb=" C CYS D 454 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.34e-02 5.57e+03 2.02e+01 bond pdb=" CA MET D 581 " pdb=" C MET D 581 " ideal model delta sigma weight residual 1.523 1.444 0.079 1.80e-02 3.09e+03 1.93e+01 ... (remaining 28119 not shown) Histogram of bond angle deviations from ideal: 81.34 - 91.99: 2 91.99 - 102.64: 223 102.64 - 113.28: 16711 113.28 - 123.93: 20612 123.93 - 134.57: 690 Bond angle restraints: 38238 Sorted by residual: angle pdb=" O3' DC T 2 " pdb=" P DA T 3 " pdb=" OP2 DA T 3 " ideal model delta sigma weight residual 108.00 81.34 26.66 3.00e+00 1.11e-01 7.89e+01 angle pdb=" O3' DC T 2 " pdb=" P DA T 3 " pdb=" OP1 DA T 3 " ideal model delta sigma weight residual 108.00 84.53 23.47 3.00e+00 1.11e-01 6.12e+01 angle pdb=" C GLY D 586 " pdb=" N LEU D 587 " pdb=" CA LEU D 587 " ideal model delta sigma weight residual 122.48 111.16 11.32 1.62e+00 3.81e-01 4.88e+01 angle pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta sigma weight residual 121.63 108.42 13.21 1.91e+00 2.74e-01 4.79e+01 angle pdb=" OP1 DA T 3 " pdb=" P DA T 3 " pdb=" OP2 DA T 3 " ideal model delta sigma weight residual 120.00 134.57 -14.57 3.00e+00 1.11e-01 2.36e+01 ... (remaining 38233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 16966 35.19 - 70.39: 206 70.39 - 105.58: 17 105.58 - 140.77: 1 140.77 - 175.97: 1 Dihedral angle restraints: 17191 sinusoidal: 7530 harmonic: 9661 Sorted by residual: dihedral pdb=" O4' U R 13 " pdb=" C1' U R 13 " pdb=" N1 U R 13 " pdb=" C2 U R 13 " ideal model delta sinusoidal sigma weight residual -160.00 -68.41 -91.59 1 1.50e+01 4.44e-03 4.38e+01 dihedral pdb=" CA THR C 757 " pdb=" C THR C 757 " pdb=" N ARG C 758 " pdb=" CA ARG C 758 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 17188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.398: 4353 0.398 - 0.796: 0 0.796 - 1.193: 0 1.193 - 1.591: 0 1.591 - 1.989: 1 Chirality restraints: 4354 Sorted by residual: chirality pdb=" P DA T 3 " pdb=" OP1 DA T 3 " pdb=" OP2 DA T 3 " pdb=" O5' DA T 3 " both_signs ideal model delta sigma weight residual True 2.35 0.36 1.99 2.00e-01 2.50e+01 9.89e+01 chirality pdb=" CA GLN C 659 " pdb=" N GLN C 659 " pdb=" C GLN C 659 " pdb=" CB GLN C 659 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE C 11 " pdb=" CA ILE C 11 " pdb=" CG1 ILE C 11 " pdb=" CG2 ILE C 11 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4351 not shown) Planarity restraints: 4805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 368 " 0.055 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO D 369 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 369 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 369 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 29 " 0.051 5.00e-02 4.00e+02 7.72e-02 9.54e+00 pdb=" N PRO A 30 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 589 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO C 590 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 590 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 590 " 0.039 5.00e-02 4.00e+02 ... (remaining 4802 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 271 2.58 - 3.16: 24745 3.16 - 3.74: 38814 3.74 - 4.32: 52856 4.32 - 4.90: 84516 Nonbonded interactions: 201202 Sorted by model distance: nonbonded pdb=" N2 DG N 38 " pdb=" O2 DC T 2 " model vdw 1.995 2.520 nonbonded pdb=" OP1 U R 11 " pdb="MG MG D1503 " model vdw 2.002 2.170 nonbonded pdb=" OG1 THR D 790 " pdb=" O2' U R 12 " model vdw 2.069 2.440 nonbonded pdb=" O GLY C 747 " pdb=" NH2 ARG C 974 " model vdw 2.090 2.520 nonbonded pdb=" OG SER C 318 " pdb=" OD1 ASP C 320 " model vdw 2.104 2.440 ... (remaining 201197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 232) selection = (chain 'B' and resid 7 through 232) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.340 Check model and map are aligned: 0.400 Set scattering table: 0.260 Process input model: 84.650 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.110 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.009 0.087 28124 Z= 0.594 Angle : 0.991 26.655 38238 Z= 0.543 Chirality : 0.059 1.989 4354 Planarity : 0.006 0.084 4805 Dihedral : 11.714 175.967 10981 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.65 % Favored : 86.32 % Rotamer: Outliers : 0.07 % Allowed : 1.05 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.12), residues: 3349 helix: -1.90 (0.13), residues: 1125 sheet: -2.52 (0.22), residues: 404 loop : -3.83 (0.11), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 183 HIS 0.009 0.002 HIS C1070 PHE 0.030 0.003 PHE C 828 TYR 0.029 0.003 TYR C1053 ARG 0.010 0.001 ARG C 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 605 time to evaluate : 3.274 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: F 76 ASP cc_start: 0.7156 (t0) cc_final: 0.6934 (t0) REVERT: B 66 HIS cc_start: 0.6972 (t70) cc_final: 0.5720 (t-90) REVERT: C 241 LEU cc_start: 0.8021 (tp) cc_final: 0.7804 (tt) REVERT: C 247 ARG cc_start: 0.7742 (ttm-80) cc_final: 0.7492 (ptt90) REVERT: C 357 ASN cc_start: 0.8911 (t0) cc_final: 0.8320 (m-40) REVERT: D 137 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7934 (mtp85) REVERT: D 564 VAL cc_start: 0.8781 (t) cc_final: 0.8581 (t) REVERT: D 1121 LEU cc_start: 0.8316 (mt) cc_final: 0.8051 (mt) outliers start: 2 outliers final: 0 residues processed: 606 average time/residue: 0.4500 time to fit residues: 408.7439 Evaluate side-chains 282 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.9980 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 305 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN C 65 ASN C 69 GLN C 150 HIS C 330 HIS C 437 ASN C 580 GLN C 628 HIS C 811 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1157 GLN C1268 GLN C1313 HIS D 232 ASN D 266 ASN D 365 GLN D 680 ASN D 792 ASN D 929 GLN D1010 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28124 Z= 0.186 Angle : 0.674 27.043 38238 Z= 0.338 Chirality : 0.053 1.942 4354 Planarity : 0.005 0.057 4805 Dihedral : 12.803 179.708 4390 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.22 % Allowed : 8.80 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 3349 helix: 0.29 (0.16), residues: 1140 sheet: -1.96 (0.24), residues: 403 loop : -3.11 (0.12), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 409 HIS 0.005 0.001 HIS C 150 PHE 0.032 0.001 PHE D1037 TYR 0.013 0.001 TYR D 512 ARG 0.006 0.001 ARG D 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 340 time to evaluate : 3.035 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: F 76 ASP cc_start: 0.7360 (t0) cc_final: 0.7079 (t0) REVERT: F 96 ASP cc_start: 0.5771 (OUTLIER) cc_final: 0.5560 (m-30) REVERT: F 109 ASP cc_start: 0.7932 (m-30) cc_final: 0.7682 (m-30) REVERT: C 239 MET cc_start: 0.8456 (tmm) cc_final: 0.8185 (ppp) REVERT: C 357 ASN cc_start: 0.8899 (t0) cc_final: 0.8367 (m-40) REVERT: C 515 MET cc_start: 0.7934 (ttp) cc_final: 0.7731 (ttp) REVERT: C 915 ASP cc_start: 0.8172 (t0) cc_final: 0.7745 (m-30) REVERT: C 997 TRP cc_start: 0.7144 (m-10) cc_final: 0.6687 (m-90) REVERT: D 264 ASP cc_start: 0.7968 (m-30) cc_final: 0.7668 (m-30) REVERT: D 372 MET cc_start: 0.8446 (mtp) cc_final: 0.7984 (ttm) REVERT: D 402 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 12 LYS cc_start: 0.8433 (tppt) cc_final: 0.8195 (tppt) outliers start: 35 outliers final: 17 residues processed: 363 average time/residue: 0.4159 time to fit residues: 237.5730 Evaluate side-chains 274 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 256 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 253 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 305 optimal weight: 0.8980 chunk 330 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 303 optimal weight: 20.0000 chunk 104 optimal weight: 0.7980 chunk 245 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C1080 ASN D 792 ASN D 979 ASN D1126 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28124 Z= 0.153 Angle : 0.597 27.069 38238 Z= 0.296 Chirality : 0.051 1.947 4354 Planarity : 0.004 0.054 4805 Dihedral : 12.626 179.035 4390 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.61 % Allowed : 11.10 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3349 helix: 1.04 (0.16), residues: 1148 sheet: -1.24 (0.24), residues: 412 loop : -2.75 (0.13), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 409 HIS 0.003 0.001 HIS D 430 PHE 0.026 0.001 PHE C 545 TYR 0.016 0.001 TYR C 367 ARG 0.009 0.000 ARG C 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 283 time to evaluate : 2.877 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: F 72 LEU cc_start: 0.8853 (mt) cc_final: 0.8358 (mt) REVERT: F 124 MET cc_start: 0.8406 (tmm) cc_final: 0.8170 (tmm) REVERT: A 117 HIS cc_start: 0.6526 (p-80) cc_final: 0.6207 (p-80) REVERT: C 108 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8029 (pm20) REVERT: C 239 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7693 (ppp) REVERT: C 331 LYS cc_start: 0.6830 (mmtm) cc_final: 0.6602 (mmtp) REVERT: C 357 ASN cc_start: 0.8936 (t0) cc_final: 0.8496 (m-40) REVERT: C 915 ASP cc_start: 0.8077 (t0) cc_final: 0.7761 (m-30) REVERT: C 1088 ASP cc_start: 0.7728 (p0) cc_final: 0.7519 (p0) REVERT: C 1290 MET cc_start: 0.8640 (tpp) cc_final: 0.8253 (tpp) REVERT: D 236 TRP cc_start: 0.8886 (m-10) cc_final: 0.8501 (m-90) REVERT: E 67 ARG cc_start: 0.8830 (ttm-80) cc_final: 0.8290 (mtp85) REVERT: E 68 GLU cc_start: 0.8437 (tp30) cc_final: 0.8079 (tp30) outliers start: 46 outliers final: 21 residues processed: 310 average time/residue: 0.3883 time to fit residues: 192.6538 Evaluate side-chains 260 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 238 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.0470 chunk 229 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 306 optimal weight: 0.0770 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 290 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 ASN F 81 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN C1209 GLN D 365 GLN D 450 HIS D 792 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28124 Z= 0.236 Angle : 0.629 27.632 38238 Z= 0.311 Chirality : 0.051 1.934 4354 Planarity : 0.004 0.060 4805 Dihedral : 12.634 179.021 4390 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.58 % Allowed : 12.39 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.14), residues: 3349 helix: 1.28 (0.16), residues: 1150 sheet: -0.82 (0.25), residues: 392 loop : -2.55 (0.13), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 183 HIS 0.006 0.001 HIS D 450 PHE 0.015 0.001 PHE F 103 TYR 0.013 0.001 TYR D 631 ARG 0.004 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 242 time to evaluate : 3.347 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: F 124 MET cc_start: 0.8426 (tmm) cc_final: 0.8039 (tmm) REVERT: A 117 HIS cc_start: 0.6500 (p-80) cc_final: 0.6185 (p-80) REVERT: A 207 THR cc_start: 0.8459 (m) cc_final: 0.8188 (p) REVERT: B 143 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7698 (mtm110) REVERT: C 108 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7960 (pm20) REVERT: C 239 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7755 (ppp) REVERT: C 357 ASN cc_start: 0.9007 (t0) cc_final: 0.8530 (m-40) REVERT: C 515 MET cc_start: 0.8057 (ttp) cc_final: 0.7787 (ttp) REVERT: C 974 ARG cc_start: 0.7633 (tpp80) cc_final: 0.7094 (tpp80) REVERT: D 1025 MET cc_start: 0.8452 (tpp) cc_final: 0.8157 (tpp) REVERT: D 1184 ASP cc_start: 0.7437 (m-30) cc_final: 0.7140 (m-30) REVERT: E 68 GLU cc_start: 0.8473 (tp30) cc_final: 0.8230 (tp30) outliers start: 74 outliers final: 40 residues processed: 296 average time/residue: 0.3929 time to fit residues: 186.1819 Evaluate side-chains 259 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 217 time to evaluate : 3.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 142 GLU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 224 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 81 optimal weight: 0.2980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 GLN ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28124 Z= 0.252 Angle : 0.631 27.325 38238 Z= 0.311 Chirality : 0.051 1.942 4354 Planarity : 0.004 0.054 4805 Dihedral : 12.712 179.749 4390 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.00 % Allowed : 13.26 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3349 helix: 1.38 (0.16), residues: 1145 sheet: -0.87 (0.25), residues: 413 loop : -2.42 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 183 HIS 0.005 0.001 HIS D 545 PHE 0.015 0.001 PHE F 112 TYR 0.021 0.001 TYR F 64 ARG 0.004 0.000 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 237 time to evaluate : 3.054 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: F 124 MET cc_start: 0.8410 (tmm) cc_final: 0.7709 (tmm) REVERT: A 117 HIS cc_start: 0.6674 (p-80) cc_final: 0.6427 (p-80) REVERT: A 207 THR cc_start: 0.8623 (m) cc_final: 0.8355 (p) REVERT: B 143 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7753 (mtm110) REVERT: C 239 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7749 (ppp) REVERT: C 335 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8359 (t) REVERT: C 357 ASN cc_start: 0.9035 (t0) cc_final: 0.8493 (m-40) REVERT: C 515 MET cc_start: 0.8100 (ttp) cc_final: 0.7791 (ttp) REVERT: C 542 ARG cc_start: 0.7100 (ttp80) cc_final: 0.6827 (ttp80) REVERT: C 696 ASP cc_start: 0.7796 (p0) cc_final: 0.6772 (t0) REVERT: C 1329 GLU cc_start: 0.7599 (tt0) cc_final: 0.6662 (tt0) REVERT: D 532 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7443 (tt0) REVERT: D 562 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6805 (pp20) REVERT: D 1025 MET cc_start: 0.8564 (tpp) cc_final: 0.8344 (tpp) REVERT: D 1184 ASP cc_start: 0.7443 (m-30) cc_final: 0.7115 (m-30) REVERT: D 1189 MET cc_start: 0.8042 (tmm) cc_final: 0.7717 (tpp) REVERT: E 55 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6980 (mm-30) REVERT: E 68 GLU cc_start: 0.8472 (tp30) cc_final: 0.8218 (tp30) outliers start: 86 outliers final: 56 residues processed: 301 average time/residue: 0.3722 time to fit residues: 181.0399 Evaluate side-chains 269 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 208 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 604 HIS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1107 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 325 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS D 680 ASN D 936 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 28124 Z= 0.433 Angle : 0.735 27.795 38238 Z= 0.367 Chirality : 0.053 1.922 4354 Planarity : 0.005 0.055 4805 Dihedral : 12.926 177.829 4390 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.35 % Allowed : 13.93 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3349 helix: 1.14 (0.16), residues: 1149 sheet: -1.04 (0.25), residues: 430 loop : -2.49 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 183 HIS 0.009 0.001 HIS D 777 PHE 0.023 0.002 PHE F 112 TYR 0.014 0.002 TYR C1087 ARG 0.005 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 214 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 124 MET cc_start: 0.8453 (tmm) cc_final: 0.7792 (tmm) REVERT: F 149 TYR cc_start: 0.7634 (m-80) cc_final: 0.7199 (m-80) REVERT: B 143 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7793 (mtm110) REVERT: C 108 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6853 (pm20) REVERT: C 239 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7750 (ppp) REVERT: C 1274 GLU cc_start: 0.7903 (mp0) cc_final: 0.7665 (mp0) REVERT: D 532 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: D 562 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: D 1025 MET cc_start: 0.8601 (tpp) cc_final: 0.8375 (tpp) REVERT: D 1184 ASP cc_start: 0.7618 (m-30) cc_final: 0.7243 (m-30) REVERT: D 1189 MET cc_start: 0.8085 (tmm) cc_final: 0.7793 (tmm) REVERT: E 8 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7797 (p0) REVERT: E 68 GLU cc_start: 0.8562 (tp30) cc_final: 0.8239 (tp30) outliers start: 96 outliers final: 61 residues processed: 289 average time/residue: 0.3570 time to fit residues: 170.7729 Evaluate side-chains 255 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 189 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 604 HIS Chi-restraints excluded: chain C residue 765 ILE Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1330 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 805 GLN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1175 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 73 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 185 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 181 optimal weight: 0.2980 chunk 323 optimal weight: 0.9990 chunk 202 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 49 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN D 680 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28124 Z= 0.146 Angle : 0.602 27.094 38238 Z= 0.296 Chirality : 0.051 1.947 4354 Planarity : 0.004 0.053 4805 Dihedral : 12.687 178.974 4390 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.09 % Allowed : 15.46 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3349 helix: 1.46 (0.16), residues: 1157 sheet: -0.69 (0.26), residues: 401 loop : -2.27 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 115 HIS 0.010 0.001 HIS D 936 PHE 0.013 0.001 PHE D 176 TYR 0.026 0.001 TYR F 64 ARG 0.006 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 239 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8805 (mt) cc_final: 0.8192 (mt) REVERT: F 124 MET cc_start: 0.8435 (tmm) cc_final: 0.7646 (tmm) REVERT: F 149 TYR cc_start: 0.7528 (m-80) cc_final: 0.7246 (m-80) REVERT: C 108 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7085 (pm20) REVERT: C 335 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8374 (t) REVERT: C 472 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 542 ARG cc_start: 0.7186 (ttp80) cc_final: 0.6908 (ttp80) REVERT: C 696 ASP cc_start: 0.7895 (p0) cc_final: 0.6946 (t0) REVERT: D 295 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: D 532 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: D 562 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6906 (pp20) REVERT: D 1184 ASP cc_start: 0.7384 (m-30) cc_final: 0.7019 (m-30) REVERT: D 1189 MET cc_start: 0.8137 (tmm) cc_final: 0.7787 (tpp) REVERT: E 68 GLU cc_start: 0.8474 (tp30) cc_final: 0.8237 (tp30) outliers start: 60 outliers final: 39 residues processed: 284 average time/residue: 0.3876 time to fit residues: 180.3028 Evaluate side-chains 252 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 73 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 205 optimal weight: 0.0980 chunk 220 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28124 Z= 0.195 Angle : 0.611 27.390 38238 Z= 0.300 Chirality : 0.051 1.936 4354 Planarity : 0.004 0.052 4805 Dihedral : 12.622 178.550 4390 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.06 % Allowed : 15.99 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3349 helix: 1.50 (0.16), residues: 1158 sheet: -0.69 (0.26), residues: 393 loop : -2.20 (0.14), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.005 0.001 HIS D 777 PHE 0.011 0.001 PHE D 176 TYR 0.022 0.001 TYR C 291 ARG 0.004 0.000 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 218 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8849 (mt) cc_final: 0.8251 (mt) REVERT: F 103 PHE cc_start: 0.7406 (p90) cc_final: 0.7199 (p90) REVERT: F 124 MET cc_start: 0.8519 (tmm) cc_final: 0.7750 (tmm) REVERT: F 149 TYR cc_start: 0.7673 (m-80) cc_final: 0.7094 (m-80) REVERT: C 472 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8359 (tm-30) REVERT: C 542 ARG cc_start: 0.7316 (ttp80) cc_final: 0.7069 (ttp80) REVERT: C 696 ASP cc_start: 0.7927 (p0) cc_final: 0.7077 (t0) REVERT: D 192 MET cc_start: 0.8883 (ttm) cc_final: 0.8673 (ttm) REVERT: D 295 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: D 532 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: D 562 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6934 (pp20) REVERT: D 697 MET cc_start: 0.8875 (ttp) cc_final: 0.8499 (tmm) REVERT: D 1184 ASP cc_start: 0.7484 (m-30) cc_final: 0.7134 (m-30) REVERT: D 1189 MET cc_start: 0.8099 (tmm) cc_final: 0.7707 (tpp) REVERT: E 68 GLU cc_start: 0.8501 (tp30) cc_final: 0.8227 (tp30) outliers start: 59 outliers final: 45 residues processed: 264 average time/residue: 0.3733 time to fit residues: 161.4237 Evaluate side-chains 257 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 209 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 562 GLU Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Chi-restraints excluded: chain E residue 73 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 8.9990 chunk 310 optimal weight: 0.2980 chunk 283 optimal weight: 0.9990 chunk 301 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 92 optimal weight: 0.0010 chunk 272 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 300 optimal weight: 0.0170 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 84 ASN D 792 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28124 Z= 0.135 Angle : 0.586 27.205 38238 Z= 0.286 Chirality : 0.050 1.948 4354 Planarity : 0.004 0.052 4805 Dihedral : 12.479 176.829 4390 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.75 % Allowed : 16.47 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3349 helix: 1.67 (0.16), residues: 1165 sheet: -0.34 (0.27), residues: 374 loop : -2.05 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 580 HIS 0.004 0.001 HIS D 865 PHE 0.011 0.001 PHE D 176 TYR 0.026 0.001 TYR F 64 ARG 0.006 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 248 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8812 (mt) cc_final: 0.8215 (mt) REVERT: F 124 MET cc_start: 0.8548 (tmm) cc_final: 0.8070 (tmm) REVERT: F 149 TYR cc_start: 0.7607 (m-80) cc_final: 0.7010 (m-80) REVERT: C 335 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8365 (t) REVERT: C 472 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8312 (tm-30) REVERT: C 696 ASP cc_start: 0.7531 (p0) cc_final: 0.6486 (t0) REVERT: C 1290 MET cc_start: 0.8640 (tpp) cc_final: 0.8290 (tpp) REVERT: D 295 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: D 532 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: D 995 TYR cc_start: 0.6448 (m-10) cc_final: 0.6084 (m-10) REVERT: D 1184 ASP cc_start: 0.7378 (m-30) cc_final: 0.7021 (m-30) REVERT: D 1189 MET cc_start: 0.8120 (tmm) cc_final: 0.7725 (tpp) REVERT: E 8 ASP cc_start: 0.8286 (p0) cc_final: 0.8014 (p0) REVERT: E 68 GLU cc_start: 0.8446 (tp30) cc_final: 0.8079 (tp30) outliers start: 50 outliers final: 37 residues processed: 288 average time/residue: 0.3609 time to fit residues: 169.2203 Evaluate side-chains 262 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 768 ASN Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 8.9990 chunk 319 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 151 optimal weight: 0.6980 chunk 221 optimal weight: 0.5980 chunk 334 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28124 Z= 0.246 Angle : 0.636 27.618 38238 Z= 0.312 Chirality : 0.051 1.933 4354 Planarity : 0.004 0.051 4805 Dihedral : 12.542 178.480 4390 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.68 % Allowed : 16.72 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.15), residues: 3349 helix: 1.66 (0.16), residues: 1153 sheet: -0.48 (0.26), residues: 396 loop : -2.01 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 183 HIS 0.005 0.001 HIS D 430 PHE 0.010 0.001 PHE C 514 TYR 0.021 0.001 TYR A 185 ARG 0.008 0.000 ARG E 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6698 Ramachandran restraints generated. 3349 Oldfield, 0 Emsley, 3349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 211 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 72 LEU cc_start: 0.8882 (mt) cc_final: 0.8251 (mt) REVERT: F 124 MET cc_start: 0.8539 (tmm) cc_final: 0.8019 (tmm) REVERT: F 149 TYR cc_start: 0.7773 (m-80) cc_final: 0.7299 (m-80) REVERT: C 335 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8321 (t) REVERT: C 472 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8354 (tm-30) REVERT: C 1274 GLU cc_start: 0.7900 (mp0) cc_final: 0.7682 (mp0) REVERT: D 295 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: D 532 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: D 995 TYR cc_start: 0.6532 (m-10) cc_final: 0.6168 (m-10) REVERT: D 1184 ASP cc_start: 0.7448 (m-30) cc_final: 0.7114 (m-30) REVERT: D 1189 MET cc_start: 0.7935 (tmm) cc_final: 0.7708 (tpp) REVERT: E 55 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7009 (mm-30) REVERT: E 68 GLU cc_start: 0.8483 (tp30) cc_final: 0.8204 (tp30) outliers start: 48 outliers final: 42 residues processed: 249 average time/residue: 0.3648 time to fit residues: 148.7790 Evaluate side-chains 250 residues out of total 2865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 86 PHE Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 423 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 997 TRP Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 768 ASN Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 936 HIS Chi-restraints excluded: chain D residue 963 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 8.9990 chunk 283 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 245 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 274 optimal weight: 0.4980 chunk 33 optimal weight: 0.0050 chunk 49 optimal weight: 0.6980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 HIS D 792 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.105716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.077527 restraints weight = 63764.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.079545 restraints weight = 35190.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079920 restraints weight = 23639.850| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 28124 Z= 0.137 Angle : 0.594 27.251 38238 Z= 0.289 Chirality : 0.050 1.947 4354 Planarity : 0.004 0.052 4805 Dihedral : 12.462 177.287 4390 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 1.64 % Allowed : 16.96 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3349 helix: 1.77 (0.16), residues: 1156 sheet: -0.36 (0.27), residues: 387 loop : -1.90 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 580 HIS 0.014 0.001 HIS A 117 PHE 0.011 0.001 PHE D 176 TYR 0.032 0.001 TYR F 64 ARG 0.008 0.000 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5033.90 seconds wall clock time: 91 minutes 58.56 seconds (5518.56 seconds total)