Starting phenix.real_space_refine on Tue Feb 20 01:04:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rip_4893/02_2024/6rip_4893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rip_4893/02_2024/6rip_4893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rip_4893/02_2024/6rip_4893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rip_4893/02_2024/6rip_4893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rip_4893/02_2024/6rip_4893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rip_4893/02_2024/6rip_4893.pdb" } resolution = 3.4 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= 0.014 sd= 0.129 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 67 5.49 5 Mg 1 5.21 5 S 106 5.16 5 C 16290 2.51 5 N 4663 2.21 5 O 5217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26346 Number of models: 1 Model: "" Number of chains: 9 Chain: "N" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 489 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "T" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 655 Classifications: {'DNA': 32} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, '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: 10397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10397 Classifications: {'peptide': 1336} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1281} Chain breaks: 2 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 15540 SG CYS D 70 108.348 56.790 73.190 1.00146.20 S ATOM 15554 SG CYS D 72 110.008 53.804 73.626 1.00153.31 S ATOM 15662 SG CYS D 85 110.800 54.956 70.520 1.00138.19 S ATOM 15686 SG CYS D 88 107.392 55.500 70.148 1.00137.51 S ATOM 21374 SG CYS D 814 86.123 119.850 75.280 1.00 76.64 S ATOM 21939 SG CYS D 888 85.234 116.499 74.532 1.00 69.93 S ATOM 21990 SG CYS D 895 85.746 117.480 77.609 1.00 64.18 S ATOM 22011 SG CYS D 898 83.026 119.027 76.884 1.00 65.10 S Time building chain proxies: 13.72, per 1000 atoms: 0.52 Number of scatterers: 26346 At special positions: 0 Unit cell: (129.107, 156.849, 166.452, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 106 16.00 P 67 15.00 Mg 1 11.99 O 5217 8.00 N 4663 7.00 C 16290 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: 10.90 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " 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 D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " Number of angles added : 12 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5880 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 45 sheets defined 38.6% alpha, 13.6% beta 30 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 8.86 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.930A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.918A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 212 through 230 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 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 Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.242A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.507A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.784A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.846A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 614' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 Processing helix chain 'C' and resid 942 through 981 removed outlier: 4.280A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.090A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.881A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 4.196A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.511A pdb=" N PHE C1164 " --> pdb=" O LEU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1177 removed outlier: 3.512A pdb=" N MET C1170 " --> pdb=" O ASP C1166 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C1172 " --> pdb=" O GLU C1168 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1284 through 1293 Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1333 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 77 through 81 Processing helix chain 'D' and resid 96 through 101 Processing helix chain 'D' and resid 113 through 118 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 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.601A pdb=" N LEU D 249 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 283 Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 489 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 597 through 613 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 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: 4.089A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.916A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1137 through 1147 Processing helix chain 'D' and resid 1216 through 1225 Processing helix chain 'D' and resid 1225 through 1244 Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1325 removed outlier: 3.945A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1338 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.616A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 7.412A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG A 182 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 6.774A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 109 removed outlier: 3.962A pdb=" N GLY A 108 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 31 removed outlier: 6.567A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 23 through 31 removed outlier: 6.567A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 202 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 6.702A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 4.181A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.776A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.776A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB5, first strand: chain 'C' and resid 452 through 453 removed outlier: 6.454A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 228 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.280A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AC2, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.620A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.334A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 834 through 835 removed outlier: 4.279A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.053A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD3, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD4, first strand: chain 'C' and resid 1336 through 1337 Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 3.808A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 707 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 826 removed outlier: 6.873A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 951 through 952 Processing sheet with id=AE3, first strand: chain 'D' and resid 957 through 961 removed outlier: 6.612A pdb=" N LEU D 982 " --> pdb=" O SER D 994 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER D 994 " --> pdb=" O LEU D 982 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU D 984 " --> pdb=" O LYS D 992 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE5, first strand: chain 'D' and resid 1033 through 1034 Processing sheet with id=AE6, first strand: chain 'D' and resid 1047 through 1049 Processing sheet with id=AE7, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE8, first strand: chain 'D' and resid 1187 through 1188 Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 1054 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 12.06 Time building geometry restraints manager: 11.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4559 1.31 - 1.43: 6693 1.43 - 1.56: 15312 1.56 - 1.68: 132 1.68 - 1.81: 184 Bond restraints: 26880 Sorted by residual: bond pdb=" CA TYR C 810 " pdb=" C TYR C 810 " ideal model delta sigma weight residual 1.522 1.389 0.133 1.72e-02 3.38e+03 5.98e+01 bond pdb=" CA GLU C 672 " pdb=" C GLU C 672 " ideal model delta sigma weight residual 1.523 1.387 0.136 1.80e-02 3.09e+03 5.74e+01 bond pdb=" C ASP C1084 " pdb=" N MET C1085 " ideal model delta sigma weight residual 1.328 1.232 0.096 1.45e-02 4.76e+03 4.35e+01 bond pdb=" CA LEU D 363 " pdb=" C LEU D 363 " ideal model delta sigma weight residual 1.523 1.421 0.102 1.80e-02 3.09e+03 3.20e+01 bond pdb=" CA THR D 514 " pdb=" CB THR D 514 " ideal model delta sigma weight residual 1.531 1.374 0.156 3.12e-02 1.03e+03 2.52e+01 ... (remaining 26875 not shown) Histogram of bond angle deviations from ideal: 81.24 - 91.80: 2 91.80 - 102.35: 220 102.35 - 112.91: 15812 112.91 - 123.47: 19550 123.47 - 134.03: 1017 Bond angle restraints: 36601 Sorted by residual: angle pdb=" O3' DG T 24 " pdb=" P DG T 25 " pdb=" OP1 DG T 25 " ideal model delta sigma weight residual 108.00 81.24 26.76 3.00e+00 1.11e-01 7.96e+01 angle pdb=" O3' DG T 24 " pdb=" P DG T 25 " pdb=" OP2 DG T 25 " ideal model delta sigma weight residual 108.00 83.39 24.61 3.00e+00 1.11e-01 6.73e+01 angle pdb=" C TYR B 152 " pdb=" N VAL B 153 " pdb=" CA VAL B 153 " ideal model delta sigma weight residual 122.85 116.44 6.41 8.70e-01 1.32e+00 5.44e+01 angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 111.91 106.31 5.60 8.90e-01 1.26e+00 3.96e+01 angle pdb=" C HIS D 897 " pdb=" N CYS D 898 " pdb=" CA CYS D 898 " ideal model delta sigma weight residual 122.31 110.62 11.69 2.00e+00 2.50e-01 3.41e+01 ... (remaining 36596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 16071 35.93 - 71.86: 311 71.86 - 107.79: 18 107.79 - 143.72: 1 143.72 - 179.65: 3 Dihedral angle restraints: 16404 sinusoidal: 7262 harmonic: 9142 Sorted by residual: dihedral pdb=" CA VAL B 19 " pdb=" C VAL B 19 " pdb=" N SER B 20 " pdb=" CA SER B 20 " ideal model delta harmonic sigma weight residual -180.00 -150.53 -29.47 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ASP C 624 " pdb=" C ASP C 624 " pdb=" N GLU C 625 " pdb=" CA GLU C 625 " ideal model delta harmonic sigma weight residual 180.00 151.18 28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ILE D 416 " pdb=" C ILE D 416 " pdb=" N ARG D 417 " pdb=" CA ARG D 417 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 16401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.383: 4184 0.383 - 0.767: 0 0.767 - 1.150: 0 1.150 - 1.534: 0 1.534 - 1.917: 1 Chirality restraints: 4185 Sorted by residual: chirality pdb=" P DG T 25 " pdb=" OP1 DG T 25 " pdb=" OP2 DG T 25 " pdb=" O5' DG T 25 " both_signs ideal model delta sigma weight residual True 2.35 0.43 1.92 2.00e-01 2.50e+01 9.19e+01 chirality pdb=" CA THR D 514 " pdb=" N THR D 514 " pdb=" C THR D 514 " pdb=" CB THR D 514 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CB THR D 514 " pdb=" CA THR D 514 " pdb=" OG1 THR D 514 " pdb=" CG2 THR D 514 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 4182 not shown) Planarity restraints: 4555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 438 " -0.061 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO D 439 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO D 439 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 439 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 450 " -0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO D 451 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 451 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 451 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 559 " -0.049 5.00e-02 4.00e+02 7.44e-02 8.85e+00 pdb=" N PRO C 560 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 560 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 560 " -0.041 5.00e-02 4.00e+02 ... (remaining 4552 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 148 2.42 - 3.04: 19105 3.04 - 3.66: 37009 3.66 - 4.28: 54470 4.28 - 4.90: 87564 Nonbonded interactions: 198296 Sorted by model distance: nonbonded pdb=" OP1 U R 11 " pdb="MG MG D1503 " model vdw 1.801 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 1.919 2.170 nonbonded pdb=" O2 DC N 39 " pdb=" N2 DG T 1 " model vdw 1.985 2.496 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1501 " model vdw 2.053 2.310 nonbonded pdb=" ND2 ASN C1072 " pdb=" OE1 GLN C1111 " model vdw 2.078 2.520 ... (remaining 198291 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 6.660 Check model and map are aligned: 0.410 Set scattering table: 0.250 Process input model: 79.310 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 : 0.016 0.156 26880 Z= 1.056 Angle : 1.268 26.763 36601 Z= 0.678 Chirality : 0.068 1.917 4185 Planarity : 0.007 0.091 4555 Dihedral : 13.548 179.653 10524 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 17.13 % Favored : 82.80 % Rotamer: Outliers : 0.18 % Allowed : 2.17 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -5.16 (0.11), residues: 3169 helix: -2.86 (0.11), residues: 1112 sheet: -2.80 (0.23), residues: 370 loop : -4.12 (0.11), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP D 115 HIS 0.017 0.003 HIS D 777 PHE 0.038 0.004 PHE C1270 TYR 0.038 0.004 TYR C1053 ARG 0.013 0.001 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 435 time to evaluate : 3.080 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: A 137 ASN cc_start: 0.8807 (p0) cc_final: 0.8430 (p0) REVERT: B 145 LYS cc_start: 0.8443 (tttt) cc_final: 0.8109 (ttmt) REVERT: C 121 GLU cc_start: 0.6844 (pt0) cc_final: 0.6547 (pp20) REVERT: C 195 PHE cc_start: 0.8521 (m-80) cc_final: 0.8114 (m-80) REVERT: C 273 HIS cc_start: 0.7883 (m170) cc_final: 0.7681 (m-70) REVERT: C 283 LYS cc_start: 0.7365 (mttt) cc_final: 0.7042 (ptmm) REVERT: C 340 ASP cc_start: 0.8148 (m-30) cc_final: 0.7787 (t0) REVERT: C 484 LEU cc_start: 0.8893 (tm) cc_final: 0.8519 (pt) REVERT: C 524 ILE cc_start: 0.9331 (tt) cc_final: 0.9128 (tp) REVERT: C 1000 LEU cc_start: 0.5430 (mt) cc_final: 0.5210 (mt) REVERT: D 1023 HIS cc_start: 0.7988 (m-70) cc_final: 0.7647 (m-70) REVERT: E 8 ASP cc_start: 0.8189 (m-30) cc_final: 0.7430 (m-30) outliers start: 5 outliers final: 2 residues processed: 439 average time/residue: 0.4683 time to fit residues: 302.4020 Evaluate side-chains 208 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 206 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 251 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 291 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 147 GLN B 227 GLN C 69 GLN C 150 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 580 GLN C 604 HIS C 760 ASN C 832 HIS C1080 ASN C1116 HIS C1256 GLN C1268 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 489 ASN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN D 817 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN D1326 GLN D1366 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26880 Z= 0.188 Angle : 0.664 26.644 36601 Z= 0.339 Chirality : 0.053 1.938 4185 Planarity : 0.005 0.064 4555 Dihedral : 15.639 179.042 4294 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.66 % Allowed : 6.92 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.88 (0.14), residues: 3169 helix: -0.40 (0.15), residues: 1108 sheet: -1.87 (0.24), residues: 399 loop : -3.12 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 115 HIS 0.006 0.001 HIS C 150 PHE 0.016 0.001 PHE A 231 TYR 0.021 0.001 TYR D 679 ARG 0.005 0.001 ARG D1330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 296 time to evaluate : 3.160 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: C 183 TRP cc_start: 0.8245 (m-10) cc_final: 0.7951 (m-10) REVERT: C 195 PHE cc_start: 0.8296 (m-80) cc_final: 0.8047 (m-80) REVERT: C 284 LEU cc_start: 0.7496 (mt) cc_final: 0.7084 (tp) REVERT: C 370 MET cc_start: 0.8964 (mmm) cc_final: 0.8718 (mmp) REVERT: C 434 ASP cc_start: 0.8542 (t0) cc_final: 0.8302 (t0) REVERT: C 1085 MET cc_start: 0.8898 (mmm) cc_final: 0.8430 (mmt) REVERT: D 330 MET cc_start: 0.8486 (ttm) cc_final: 0.8205 (mtp) REVERT: D 913 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7028 (mm-30) REVERT: D 1187 GLU cc_start: 0.8856 (pp20) cc_final: 0.8455 (tm-30) REVERT: E 70 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7956 (tm-30) outliers start: 45 outliers final: 16 residues processed: 327 average time/residue: 0.3875 time to fit residues: 198.8894 Evaluate side-chains 213 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 197 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 814 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 242 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 292 optimal weight: 0.9990 chunk 315 optimal weight: 0.9980 chunk 260 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 437 ASN C 760 ASN C 811 ASN C 965 GLN C1146 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 777 HIS D 792 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26880 Z= 0.318 Angle : 0.654 26.836 36601 Z= 0.333 Chirality : 0.053 1.928 4185 Planarity : 0.004 0.056 4555 Dihedral : 15.448 176.733 4292 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.95 % Allowed : 9.54 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.13 (0.14), residues: 3169 helix: 0.36 (0.16), residues: 1113 sheet: -1.50 (0.24), residues: 415 loop : -2.78 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 807 HIS 0.008 0.001 HIS B 23 PHE 0.018 0.002 PHE D 620 TYR 0.021 0.002 TYR D 382 ARG 0.005 0.000 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 TRP cc_start: 0.8268 (m-10) cc_final: 0.8040 (m-10) REVERT: C 195 PHE cc_start: 0.8352 (m-80) cc_final: 0.8087 (m-80) REVERT: C 284 LEU cc_start: 0.7587 (mt) cc_final: 0.7178 (tp) REVERT: C 314 ASN cc_start: 0.6681 (OUTLIER) cc_final: 0.6468 (t0) REVERT: C 315 MET cc_start: 0.7535 (mmm) cc_final: 0.7252 (mmm) REVERT: C 484 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (pt) REVERT: C 1329 GLU cc_start: 0.7670 (tt0) cc_final: 0.7191 (tt0) REVERT: D 697 MET cc_start: 0.8618 (ttp) cc_final: 0.8214 (tmm) REVERT: D 725 MET cc_start: 0.8608 (mtp) cc_final: 0.8405 (mtp) REVERT: D 1174 ARG cc_start: 0.6553 (ttp80) cc_final: 0.6139 (ttp80) REVERT: E 62 GLN cc_start: 0.8341 (tp40) cc_final: 0.7738 (tm-30) outliers start: 53 outliers final: 24 residues processed: 247 average time/residue: 0.3560 time to fit residues: 143.8846 Evaluate side-chains 212 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 613 ASN Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 8 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 0.0070 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 310 optimal weight: 0.0970 chunk 153 optimal weight: 4.9990 chunk 277 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN B 66 HIS C 314 ASN C 437 ASN C 811 ASN C 965 GLN D 200 GLN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26880 Z= 0.170 Angle : 0.584 26.544 36601 Z= 0.295 Chirality : 0.051 1.927 4185 Planarity : 0.004 0.048 4555 Dihedral : 15.283 177.269 4292 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.80 % Allowed : 11.01 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.56 (0.15), residues: 3169 helix: 0.86 (0.16), residues: 1117 sheet: -1.20 (0.25), residues: 415 loop : -2.46 (0.14), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 807 HIS 0.005 0.001 HIS D 777 PHE 0.011 0.001 PHE A 231 TYR 0.019 0.001 TYR D 679 ARG 0.002 0.000 ARG D1224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 3.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 183 TRP cc_start: 0.8179 (m-10) cc_final: 0.7580 (m-10) REVERT: C 195 PHE cc_start: 0.8244 (m-80) cc_final: 0.7939 (m-80) REVERT: C 284 LEU cc_start: 0.7847 (mt) cc_final: 0.7369 (tp) REVERT: C 315 MET cc_start: 0.7342 (mmm) cc_final: 0.7073 (mmm) REVERT: C 484 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8351 (pt) REVERT: C 542 ARG cc_start: 0.7872 (mmp80) cc_final: 0.7494 (mmp80) REVERT: C 600 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8627 (p) REVERT: C 960 LEU cc_start: 0.8273 (tt) cc_final: 0.7519 (tt) REVERT: C 965 GLN cc_start: 0.7670 (tp40) cc_final: 0.7450 (tp-100) REVERT: D 29 MET cc_start: 0.7791 (mmm) cc_final: 0.7549 (tmm) REVERT: D 298 MET cc_start: 0.7804 (mtm) cc_final: 0.7575 (ttm) REVERT: D 1174 ARG cc_start: 0.6491 (ttp80) cc_final: 0.5960 (tpp80) REVERT: E 3 ARG cc_start: 0.6857 (tpm170) cc_final: 0.6574 (tpt170) REVERT: E 42 GLU cc_start: 0.7841 (mp0) cc_final: 0.7468 (mp0) REVERT: E 62 GLN cc_start: 0.8339 (tp40) cc_final: 0.7738 (tm-30) outliers start: 49 outliers final: 27 residues processed: 248 average time/residue: 0.3639 time to fit residues: 147.2085 Evaluate side-chains 216 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 264 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 227 GLN C 314 ASN C 437 ASN C1209 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26880 Z= 0.284 Angle : 0.616 26.487 36601 Z= 0.310 Chirality : 0.052 1.938 4185 Planarity : 0.004 0.047 4555 Dihedral : 15.258 178.129 4292 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.14 % Allowed : 11.64 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.35 (0.15), residues: 3169 helix: 0.96 (0.16), residues: 1116 sheet: -0.97 (0.25), residues: 425 loop : -2.32 (0.14), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 580 HIS 0.005 0.001 HIS D 777 PHE 0.018 0.001 PHE D 176 TYR 0.016 0.001 TYR D 631 ARG 0.006 0.000 ARG D1174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 199 time to evaluate : 2.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.8579 (tp40) cc_final: 0.8333 (tp40) REVERT: C 132 ASP cc_start: 0.8021 (t0) cc_final: 0.7761 (t0) REVERT: C 183 TRP cc_start: 0.8261 (m-10) cc_final: 0.8047 (m-10) REVERT: C 195 PHE cc_start: 0.8375 (m-80) cc_final: 0.8032 (m-80) REVERT: C 284 LEU cc_start: 0.7854 (mt) cc_final: 0.7465 (tp) REVERT: C 315 MET cc_start: 0.7459 (mmm) cc_final: 0.7184 (mmm) REVERT: C 484 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8469 (pt) REVERT: C 542 ARG cc_start: 0.7918 (mmp80) cc_final: 0.7535 (mmp80) REVERT: C 600 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8548 (p) REVERT: D 158 GLN cc_start: 0.7214 (mp10) cc_final: 0.6903 (mp10) REVERT: D 698 MET cc_start: 0.7961 (mmm) cc_final: 0.7760 (tpp) REVERT: D 709 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6613 (ptm160) REVERT: D 807 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8959 (tt) REVERT: D 1095 MET cc_start: 0.5142 (ttt) cc_final: 0.4871 (tpp) REVERT: E 8 ASP cc_start: 0.7922 (p0) cc_final: 0.7552 (p0) REVERT: E 42 GLU cc_start: 0.7907 (mp0) cc_final: 0.7560 (mp0) REVERT: E 62 GLN cc_start: 0.8395 (tp40) cc_final: 0.7663 (tm-30) outliers start: 58 outliers final: 36 residues processed: 247 average time/residue: 0.3650 time to fit residues: 147.6073 Evaluate side-chains 225 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 10 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.0980 chunk 279 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN C 314 ASN C1209 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26880 Z= 0.193 Angle : 0.581 26.345 36601 Z= 0.291 Chirality : 0.051 1.936 4185 Planarity : 0.004 0.042 4555 Dihedral : 15.161 179.684 4292 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.10 % Allowed : 12.38 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.06 (0.15), residues: 3169 helix: 1.17 (0.16), residues: 1118 sheet: -0.70 (0.25), residues: 415 loop : -2.15 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 33 HIS 0.006 0.001 HIS D 777 PHE 0.012 0.001 PHE D 172 TYR 0.018 0.001 TYR D 631 ARG 0.004 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLN cc_start: 0.8572 (tp40) cc_final: 0.8348 (tp40) REVERT: C 132 ASP cc_start: 0.8015 (t0) cc_final: 0.7768 (t0) REVERT: C 183 TRP cc_start: 0.8218 (m-10) cc_final: 0.7882 (m-10) REVERT: C 195 PHE cc_start: 0.8339 (m-80) cc_final: 0.8040 (m-80) REVERT: C 284 LEU cc_start: 0.7731 (mt) cc_final: 0.7385 (tp) REVERT: C 315 MET cc_start: 0.7413 (mmm) cc_final: 0.7142 (mmm) REVERT: C 542 ARG cc_start: 0.7862 (mmp80) cc_final: 0.7495 (mmp80) REVERT: C 600 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8481 (p) REVERT: C 965 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7583 (tp-100) REVERT: D 158 GLN cc_start: 0.7150 (mp10) cc_final: 0.6827 (mp10) REVERT: D 298 MET cc_start: 0.7848 (mtm) cc_final: 0.7619 (ttm) REVERT: D 807 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8936 (tt) REVERT: D 1095 MET cc_start: 0.5183 (ttt) cc_final: 0.4950 (tpp) REVERT: E 8 ASP cc_start: 0.7933 (p0) cc_final: 0.6548 (p0) REVERT: E 42 GLU cc_start: 0.7883 (mp0) cc_final: 0.7492 (mp0) REVERT: E 55 GLU cc_start: 0.7893 (tp30) cc_final: 0.7189 (tp30) REVERT: E 62 GLN cc_start: 0.8382 (tp40) cc_final: 0.7674 (tm-30) outliers start: 57 outliers final: 34 residues processed: 248 average time/residue: 0.3559 time to fit residues: 146.1363 Evaluate side-chains 225 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 189 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 309 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN C 314 ASN C 965 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26880 Z= 0.187 Angle : 0.571 26.276 36601 Z= 0.285 Chirality : 0.051 1.944 4185 Planarity : 0.004 0.042 4555 Dihedral : 15.046 179.290 4292 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.36 % Allowed : 12.71 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.87 (0.15), residues: 3169 helix: 1.31 (0.16), residues: 1120 sheet: -0.62 (0.26), residues: 416 loop : -2.02 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 580 HIS 0.006 0.001 HIS D 777 PHE 0.022 0.001 PHE D 176 TYR 0.024 0.001 TYR D 46 ARG 0.003 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 198 time to evaluate : 3.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8561 (p0) cc_final: 0.8172 (p0) REVERT: C 183 TRP cc_start: 0.8205 (m-10) cc_final: 0.7867 (m-10) REVERT: C 284 LEU cc_start: 0.7868 (mt) cc_final: 0.7555 (tp) REVERT: C 315 MET cc_start: 0.7439 (mmm) cc_final: 0.7178 (mmm) REVERT: C 515 MET cc_start: 0.8179 (ttp) cc_final: 0.7937 (ttp) REVERT: C 542 ARG cc_start: 0.7834 (mmp80) cc_final: 0.7488 (mmp80) REVERT: C 704 MET cc_start: 0.8028 (mmm) cc_final: 0.7790 (mtp) REVERT: C 965 GLN cc_start: 0.7788 (tp40) cc_final: 0.7494 (tp-100) REVERT: D 298 MET cc_start: 0.7853 (mtm) cc_final: 0.7609 (ttm) REVERT: D 709 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7261 (ptm160) REVERT: D 763 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: D 807 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8923 (tt) REVERT: D 913 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6896 (mm-30) REVERT: D 1095 MET cc_start: 0.5202 (ttt) cc_final: 0.4978 (tpp) REVERT: E 42 GLU cc_start: 0.7969 (mp0) cc_final: 0.7677 (mp0) REVERT: E 62 GLN cc_start: 0.8381 (tp40) cc_final: 0.7769 (tm-30) outliers start: 64 outliers final: 40 residues processed: 249 average time/residue: 0.3673 time to fit residues: 149.9998 Evaluate side-chains 232 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 210 optimal weight: 0.0970 chunk 152 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 243 optimal weight: 0.6980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C1209 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26880 Z= 0.257 Angle : 0.606 26.226 36601 Z= 0.301 Chirality : 0.051 1.945 4185 Planarity : 0.004 0.041 4555 Dihedral : 15.044 178.306 4292 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.03 % Allowed : 13.63 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.87 (0.15), residues: 3169 helix: 1.26 (0.16), residues: 1120 sheet: -0.66 (0.25), residues: 432 loop : -1.98 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 580 HIS 0.005 0.001 HIS D 777 PHE 0.015 0.001 PHE D 172 TYR 0.026 0.001 TYR D 679 ARG 0.003 0.000 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 194 time to evaluate : 3.020 Fit side-chains revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8580 (p0) cc_final: 0.8111 (p0) REVERT: B 158 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6910 (mtt-85) REVERT: C 183 TRP cc_start: 0.8255 (m-10) cc_final: 0.7929 (m-10) REVERT: C 284 LEU cc_start: 0.7791 (mt) cc_final: 0.7525 (tp) REVERT: C 315 MET cc_start: 0.7488 (mmm) cc_final: 0.7220 (mmm) REVERT: C 542 ARG cc_start: 0.7880 (mmp80) cc_final: 0.7473 (mmp80) REVERT: C 600 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8426 (p) REVERT: C 965 GLN cc_start: 0.7749 (tp40) cc_final: 0.7414 (tp-100) REVERT: D 298 MET cc_start: 0.7855 (mtm) cc_final: 0.7583 (ttm) REVERT: D 807 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8976 (tt) REVERT: D 913 GLU cc_start: 0.7248 (mm-30) cc_final: 0.7020 (mm-30) REVERT: D 1095 MET cc_start: 0.5227 (ttt) cc_final: 0.5001 (tpp) REVERT: D 1174 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.6144 (tpp80) REVERT: E 42 GLU cc_start: 0.7956 (mp0) cc_final: 0.7634 (mp0) REVERT: E 55 GLU cc_start: 0.7920 (tp30) cc_final: 0.7272 (tp30) REVERT: E 62 GLN cc_start: 0.8386 (tp40) cc_final: 0.7783 (tm-30) REVERT: E 71 GLU cc_start: 0.8697 (tt0) cc_final: 0.8144 (tt0) outliers start: 55 outliers final: 44 residues processed: 242 average time/residue: 0.3960 time to fit residues: 152.3653 Evaluate side-chains 231 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 183 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1174 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.9990 chunk 296 optimal weight: 20.0000 chunk 270 optimal weight: 0.9990 chunk 288 optimal weight: 20.0000 chunk 173 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 287 optimal weight: 20.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 580 GLN C1157 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN E 70 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 26880 Z= 0.397 Angle : 0.684 26.067 36601 Z= 0.343 Chirality : 0.053 1.944 4185 Planarity : 0.004 0.044 4555 Dihedral : 15.170 177.324 4292 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.06 % Allowed : 13.78 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.05 (0.15), residues: 3169 helix: 1.01 (0.16), residues: 1126 sheet: -0.63 (0.26), residues: 426 loop : -2.05 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 409 HIS 0.007 0.001 HIS D 545 PHE 0.022 0.002 PHE D 176 TYR 0.023 0.002 TYR D 679 ARG 0.005 0.000 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 192 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8588 (p0) cc_final: 0.7921 (p0) REVERT: B 158 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6953 (mtt-85) REVERT: C 284 LEU cc_start: 0.7699 (mt) cc_final: 0.7421 (tp) REVERT: C 315 MET cc_start: 0.7596 (mmm) cc_final: 0.7312 (mmm) REVERT: C 600 THR cc_start: 0.8884 (OUTLIER) cc_final: 0.8437 (p) REVERT: C 965 GLN cc_start: 0.7715 (tp40) cc_final: 0.7361 (tp-100) REVERT: D 298 MET cc_start: 0.7829 (mtm) cc_final: 0.7541 (ttm) REVERT: D 807 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9027 (tt) REVERT: D 1095 MET cc_start: 0.5511 (ttt) cc_final: 0.5224 (tpp) REVERT: E 42 GLU cc_start: 0.7947 (mp0) cc_final: 0.7656 (mp0) REVERT: E 62 GLN cc_start: 0.8417 (tp40) cc_final: 0.7816 (tm-30) outliers start: 56 outliers final: 44 residues processed: 236 average time/residue: 0.3953 time to fit residues: 150.3935 Evaluate side-chains 228 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 807 LEU Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.5980 chunk 304 optimal weight: 1.9990 chunk 186 optimal weight: 0.3980 chunk 144 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 294 optimal weight: 7.9990 chunk 254 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN C 314 ASN C1209 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26880 Z= 0.161 Angle : 0.590 26.024 36601 Z= 0.294 Chirality : 0.050 1.924 4185 Planarity : 0.004 0.047 4555 Dihedral : 14.981 176.142 4292 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.69 % Allowed : 14.33 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.73 (0.15), residues: 3169 helix: 1.34 (0.16), residues: 1119 sheet: -0.50 (0.26), residues: 422 loop : -1.88 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 580 HIS 0.008 0.001 HIS D 777 PHE 0.021 0.001 PHE D 172 TYR 0.025 0.001 TYR D 679 ARG 0.003 0.000 ARG C 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6338 Ramachandran restraints generated. 3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 199 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8597 (p0) cc_final: 0.7986 (p0) REVERT: C 183 TRP cc_start: 0.8163 (m-10) cc_final: 0.7851 (m-10) REVERT: C 284 LEU cc_start: 0.7683 (mt) cc_final: 0.7453 (tp) REVERT: C 542 ARG cc_start: 0.7868 (mmp80) cc_final: 0.6150 (mmp80) REVERT: C 600 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8395 (p) REVERT: D 298 MET cc_start: 0.7810 (mtm) cc_final: 0.7556 (ttm) REVERT: D 601 ILE cc_start: 0.8778 (tt) cc_final: 0.8549 (mt) REVERT: D 1095 MET cc_start: 0.5299 (ttt) cc_final: 0.5063 (tpp) REVERT: E 8 ASP cc_start: 0.7604 (p0) cc_final: 0.7274 (p0) REVERT: E 42 GLU cc_start: 0.7845 (mp0) cc_final: 0.7564 (mp0) REVERT: E 62 GLN cc_start: 0.8382 (tp40) cc_final: 0.7854 (tm-30) outliers start: 46 outliers final: 35 residues processed: 236 average time/residue: 0.3806 time to fit residues: 145.5079 Evaluate side-chains 226 residues out of total 2715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 514 PHE Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 830 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1143 ASP Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 234 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 255 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.113575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079736 restraints weight = 53422.188| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.80 r_work: 0.2994 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26880 Z= 0.346 Angle : 0.650 25.920 36601 Z= 0.324 Chirality : 0.052 1.937 4185 Planarity : 0.004 0.044 4555 Dihedral : 15.044 175.989 4292 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.58 % Allowed : 14.40 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3169 helix: 1.18 (0.16), residues: 1123 sheet: -0.50 (0.26), residues: 422 loop : -1.91 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 409 HIS 0.006 0.001 HIS A 23 PHE 0.022 0.002 PHE D 176 TYR 0.023 0.001 TYR D 679 ARG 0.005 0.000 ARG C1246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5014.65 seconds wall clock time: 92 minutes 6.31 seconds (5526.31 seconds total)