Starting phenix.real_space_refine on Mon Sep 14 00:01:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_4893.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_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 { model { file = "/net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_4893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_4893.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_4893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_4893.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_4893.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rip_4893/09_2026/6rip_4893.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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. Time to flip 3 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'RNAv2': 13} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 7} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: 5.58, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 919.9 milliseconds 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: 2.74 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: 6.26 Time building geometry restraints manager: 2.90 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=" C3' DT T 18 " pdb=" O3' DT T 18 " ideal model delta sigma weight residual 1.435 1.367 0.068 1.30e-02 5.92e+03 2.70e+01 ... (remaining 26875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.35: 36352 5.35 - 10.71: 236 10.71 - 16.06: 10 16.06 - 21.41: 1 21.41 - 26.76: 2 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=" O4' DC T 19 " pdb=" C4' DC T 19 " pdb=" C3' DC T 19 " ideal model delta sigma weight residual 106.00 101.36 4.64 6.00e-01 2.78e+00 5.98e+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=" O4' DC T 21 " pdb=" C4' DC T 21 " pdb=" C3' DC T 21 " ideal model delta sigma weight residual 106.00 101.93 4.07 6.00e-01 2.78e+00 4.60e+01 ... (remaining 36596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 16044 35.93 - 71.86: 291 71.86 - 107.79: 15 107.79 - 143.72: 1 143.72 - 179.65: 3 Dihedral angle restraints: 16354 sinusoidal: 7212 harmonic: 9142 Sorted by residual: dihedral pdb=" O5' A R 3 " pdb=" C5' A R 3 " pdb=" C4' A R 3 " pdb=" C3' A R 3 " ideal model delta sinusoidal sigma weight residual 60.00 117.53 -57.53 3 6.40e+00 2.44e-02 5.19e+01 dihedral pdb=" O5' U R 1 " pdb=" C5' U R 1 " pdb=" C4' U R 1 " pdb=" C3' U R 1 " ideal model delta sinusoidal sigma weight residual 60.00 107.70 -47.70 3 6.40e+00 2.44e-02 4.69e+01 dihedral pdb=" O5' G R 4 " pdb=" C5' G R 4 " pdb=" C4' G R 4 " pdb=" C3' G R 4 " ideal model delta sinusoidal sigma weight residual 180.00 133.21 46.79 3 6.40e+00 2.44e-02 4.61e+01 ... (remaining 16351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 4184 0.381 - 0.763: 0 0.763 - 1.144: 0 1.144 - 1.525: 0 1.525 - 1.907: 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 2.34 0.43 1.91 2.00e-01 2.50e+01 9.09e+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 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 0.010 Normalize map: mean=0, sd=1: 1.520 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 30.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.017 0.635 26888 Z= 0.760 Angle : 1.345 47.957 36613 Z= 0.711 Chirality : 0.070 1.907 4185 Planarity : 0.007 0.091 4555 Dihedral : 13.303 179.653 10474 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.013 0.001 ARG C 529 TYR 0.038 0.004 TYR C1053 PHE 0.038 0.004 PHE C1270 TRP 0.033 0.004 TRP D 115 HIS 0.017 0.003 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.01625 / 0.75 (26880) covalent geometry : angle 1.27935 / 0.71 (36601) hydrogen bonds : bond 0.11448 / 12.67 ( 1109) hydrogen bonds : angle 7.22675 / 8.11 ( 3051) metal coordination : bond 0.24667 / 24.54 ( 8) metal coordination : angle 23.00236 / 37.82 ( 12) *********************** 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 to be fit. rotamer outliers: 5 poor density : 435 time to evaluate : 1.039 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: 0.7366 (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: 0.7989 (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: 0.2212 time to fit residues: 143.6328 Evaluate side-chains 208 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 HIS B 23 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 227 GLN C 69 GLN C 150 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 832 HIS C1080 ASN C1116 HIS C1256 GLN C1268 GLN D 200 GLN D 266 ASN D 777 HIS D 865 HIS D 875 ASN D1010 GLN D1366 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.114316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078475 restraints weight = 56183.519| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.85 r_work: 0.3057 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26888 Z= 0.167 Angle : 0.796 27.975 36613 Z= 0.399 Chirality : 0.058 1.951 4185 Planarity : 0.006 0.061 4555 Dihedral : 15.347 179.359 4244 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.62 % Allowed : 6.89 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.13), residues: 3169 helix: -0.77 (0.15), residues: 1107 sheet: -1.93 (0.24), residues: 402 loop : -3.15 (0.13), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1330 TYR 0.021 0.002 TYR D 679 PHE 0.019 0.002 PHE D 49 TRP 0.014 0.002 TRP D 115 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (26880) covalent geometry : angle 0.76986 / 0.40 (36601) hydrogen bonds : bond 0.06611 / 7.24 ( 1109) hydrogen bonds : angle 5.48356 / 6.11 ( 3051) metal coordination : bond 0.02266 / 2.07 ( 8) metal coordination : angle 11.11315 / 14.28 ( 12) *********************** 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 312 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8965 (p0) cc_final: 0.8647 (p0) REVERT: B 145 LYS cc_start: 0.8361 (tttt) cc_final: 0.8153 (ttmt) REVERT: C 121 GLU cc_start: 0.6684 (pt0) cc_final: 0.6307 (pp20) REVERT: C 183 TRP cc_start: 0.8626 (m-10) cc_final: 0.8383 (m-10) REVERT: C 195 PHE cc_start: 0.8480 (m-80) cc_final: 0.8159 (m-80) REVERT: C 283 LYS cc_start: 0.7110 (mttt) cc_final: 0.6468 (ptmm) REVERT: C 349 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7350 (tm-30) REVERT: C 370 MET cc_start: 0.8940 (mmm) cc_final: 0.8597 (mmp) REVERT: C 434 ASP cc_start: 0.9005 (t0) cc_final: 0.8699 (t0) REVERT: C 493 ILE cc_start: 0.8793 (pt) cc_final: 0.8518 (pt) REVERT: C 963 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 1274 GLU cc_start: 0.8335 (mp0) cc_final: 0.8021 (mp0) REVERT: D 298 MET cc_start: 0.7901 (mmt) cc_final: 0.7486 (mtm) REVERT: D 330 MET cc_start: 0.8966 (ttm) cc_final: 0.8101 (ttm) REVERT: D 479 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8060 (mt-10) REVERT: D 932 MET cc_start: 0.8719 (tpp) cc_final: 0.8235 (tpp) REVERT: D 999 TYR cc_start: 0.7946 (t80) cc_final: 0.7732 (t80) REVERT: D 1023 HIS cc_start: 0.8066 (m-70) cc_final: 0.7695 (m-70) REVERT: D 1361 THR cc_start: 0.7580 (OUTLIER) cc_final: 0.6940 (m) REVERT: E 3 ARG cc_start: 0.7476 (tpm170) cc_final: 0.6999 (tpt170) REVERT: E 42 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8071 (mp0) REVERT: E 62 GLN cc_start: 0.8469 (tp40) cc_final: 0.7933 (tm-30) outliers start: 44 outliers final: 20 residues processed: 300 average time/residue: 0.1801 time to fit residues: 86.5168 Evaluate side-chains 226 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 217 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 291 TYR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 609 ILE 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 C residue 1332 SER Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 1233 ILE Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1361 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 61 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 4 optimal weight: 40.0000 chunk 256 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 289 optimal weight: 20.0000 chunk 75 optimal weight: 0.1980 chunk 153 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 811 ASN C 932 GLN D 792 ASN E 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.121185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086839 restraints weight = 58751.190| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.67 r_work: 0.3130 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26888 Z= 0.137 Angle : 0.682 25.929 36613 Z= 0.340 Chirality : 0.055 1.934 4185 Planarity : 0.004 0.054 4555 Dihedral : 14.978 178.596 4242 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.95 % Allowed : 8.40 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.14), residues: 3169 helix: 0.21 (0.16), residues: 1105 sheet: -1.46 (0.24), residues: 417 loop : -2.68 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 974 TYR 0.020 0.001 TYR D 382 PHE 0.013 0.001 PHE C 505 TRP 0.007 0.001 TRP D 409 HIS 0.009 0.001 HIS C 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (26880) covalent geometry : angle 0.66589 / 0.34 (36601) hydrogen bonds : bond 0.05630 / 6.12 ( 1109) hydrogen bonds : angle 5.00240 / 5.59 ( 3051) metal coordination : bond 0.01228 / 0.90 ( 8) metal coordination : angle 8.10259 / 12.04 ( 12) *********************** 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 293 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.9082 (m) cc_final: 0.8859 (p) REVERT: B 226 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 121 GLU cc_start: 0.6568 (pt0) cc_final: 0.6282 (pp20) REVERT: C 183 TRP cc_start: 0.8603 (m-10) cc_final: 0.8377 (m-10) REVERT: C 195 PHE cc_start: 0.8497 (m-80) cc_final: 0.8209 (m-80) REVERT: C 284 LEU cc_start: 0.7649 (mt) cc_final: 0.7257 (tp) REVERT: C 315 MET cc_start: 0.7464 (mmm) cc_final: 0.7241 (mmm) REVERT: C 349 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7377 (tm-30) REVERT: C 370 MET cc_start: 0.8982 (mmm) cc_final: 0.8714 (mmp) REVERT: C 434 ASP cc_start: 0.8943 (t0) cc_final: 0.8718 (t0) REVERT: C 458 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8258 (mt-10) REVERT: C 484 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8453 (pt) REVERT: C 493 ILE cc_start: 0.8858 (pt) cc_final: 0.8603 (pt) REVERT: C 932 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7968 (mt0) REVERT: C 1274 GLU cc_start: 0.8243 (mp0) cc_final: 0.7907 (mp0) REVERT: C 1329 GLU cc_start: 0.8347 (tt0) cc_final: 0.7920 (tt0) REVERT: D 29 MET cc_start: 0.8384 (tpt) cc_final: 0.8101 (tmm) REVERT: D 91 GLU cc_start: 0.8115 (tt0) cc_final: 0.7385 (pp20) REVERT: D 298 MET cc_start: 0.7837 (mmt) cc_final: 0.7514 (mtm) REVERT: D 697 MET cc_start: 0.8572 (ttp) cc_final: 0.8313 (tmm) REVERT: D 822 MET cc_start: 0.8300 (mmm) cc_final: 0.7948 (mmm) REVERT: D 1023 HIS cc_start: 0.8052 (m-70) cc_final: 0.7693 (m-70) REVERT: D 1095 MET cc_start: 0.5429 (ttt) cc_final: 0.5171 (tpp) REVERT: D 1187 GLU cc_start: 0.8974 (pp20) cc_final: 0.8672 (tm-30) REVERT: D 1361 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7327 (p) REVERT: E 3 ARG cc_start: 0.7501 (tpm170) cc_final: 0.6922 (tpt170) REVERT: E 42 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8055 (mp0) outliers start: 53 outliers final: 25 residues processed: 284 average time/residue: 0.1782 time to fit residues: 81.4222 Evaluate side-chains 223 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 458 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 811 ASN Chi-restraints excluded: chain C residue 932 GLN 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 C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU 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 514 THR Chi-restraints excluded: chain D residue 532 GLU Chi-restraints excluded: chain D residue 802 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 D residue 1361 THR Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 240 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 264 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 291 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN D 777 HIS D 792 ASN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.114949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078726 restraints weight = 56120.922| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.86 r_work: 0.3058 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26888 Z= 0.132 Angle : 0.641 25.775 36613 Z= 0.323 Chirality : 0.054 1.943 4185 Planarity : 0.004 0.056 4555 Dihedral : 14.843 179.018 4242 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 1.92 % Allowed : 10.42 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.15), residues: 3169 helix: 0.48 (0.16), residues: 1114 sheet: -1.17 (0.25), residues: 409 loop : -2.42 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1174 TYR 0.020 0.001 TYR D 679 PHE 0.013 0.001 PHE C 505 TRP 0.006 0.001 TRP D 580 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (26880) covalent geometry : angle 0.63226 / 0.32 (36601) hydrogen bonds : bond 0.05420 / 5.87 ( 1109) hydrogen bonds : angle 4.82731 / 5.43 ( 3051) metal coordination : bond 0.00775 / 0.69 ( 8) metal coordination : angle 5.92395 / 8.68 ( 12) *********************** 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 266 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8202 (tt0) REVERT: B 226 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8165 (mt-10) REVERT: C 121 GLU cc_start: 0.6787 (pt0) cc_final: 0.6395 (pp20) REVERT: C 183 TRP cc_start: 0.8605 (m-10) cc_final: 0.8039 (m-10) REVERT: C 195 PHE cc_start: 0.8531 (m-80) cc_final: 0.8206 (m-80) REVERT: C 284 LEU cc_start: 0.7479 (mt) cc_final: 0.7166 (tp) REVERT: C 315 MET cc_start: 0.7474 (mmm) cc_final: 0.7243 (mmm) REVERT: C 349 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7458 (tm-30) REVERT: C 434 ASP cc_start: 0.9029 (t0) cc_final: 0.8812 (t0) REVERT: C 484 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8389 (pt) REVERT: C 493 ILE cc_start: 0.8727 (pt) cc_final: 0.8469 (pt) REVERT: C 542 ARG cc_start: 0.8055 (mmp80) cc_final: 0.7772 (mmp80) REVERT: C 600 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8624 (p) REVERT: C 930 ASP cc_start: 0.8396 (t0) cc_final: 0.8053 (t0) REVERT: C 963 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7875 (tm-30) REVERT: C 1274 GLU cc_start: 0.8328 (mp0) cc_final: 0.7986 (mp0) REVERT: C 1329 GLU cc_start: 0.8417 (tt0) cc_final: 0.7784 (tt0) REVERT: D 29 MET cc_start: 0.8413 (tpt) cc_final: 0.8040 (tmm) REVERT: D 91 GLU cc_start: 0.8098 (tt0) cc_final: 0.7346 (pp20) REVERT: D 235 GLU cc_start: 0.8961 (pm20) cc_final: 0.8650 (pm20) REVERT: D 298 MET cc_start: 0.7885 (mmt) cc_final: 0.7535 (mtm) REVERT: D 697 MET cc_start: 0.8588 (ttp) cc_final: 0.8365 (tmm) REVERT: D 822 MET cc_start: 0.8347 (mmm) cc_final: 0.7987 (mmm) REVERT: D 923 ILE cc_start: 0.9338 (mt) cc_final: 0.9058 (mt) REVERT: D 1095 MET cc_start: 0.5419 (ttt) cc_final: 0.5159 (tpp) REVERT: D 1174 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.5572 (mtp-110) REVERT: D 1187 GLU cc_start: 0.9000 (pp20) cc_final: 0.8632 (tm-30) REVERT: E 8 ASP cc_start: 0.8135 (p0) cc_final: 0.7720 (p0) REVERT: E 42 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8014 (mp0) outliers start: 52 outliers final: 28 residues processed: 259 average time/residue: 0.1617 time to fit residues: 69.1734 Evaluate side-chains 228 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 217 ILE Chi-restraints excluded: chain C residue 287 VAL 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 609 ILE Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 741 MET 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 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 317 THR 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 624 ILE Chi-restraints excluded: chain D residue 717 VAL 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 Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 130 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 167 optimal weight: 0.0270 chunk 92 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 66 HIS C 65 ASN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 811 ASN D 777 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.117934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.082175 restraints weight = 55677.471| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.97 r_work: 0.3128 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 26888 Z= 0.116 Angle : 0.614 25.746 36613 Z= 0.310 Chirality : 0.053 1.966 4185 Planarity : 0.004 0.048 4555 Dihedral : 14.690 179.624 4242 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.99 % Allowed : 10.90 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 3169 helix: 0.80 (0.16), residues: 1113 sheet: -0.80 (0.26), residues: 412 loop : -2.15 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1174 TYR 0.020 0.001 TYR D 679 PHE 0.013 0.001 PHE D 620 TRP 0.007 0.001 TRP D 580 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (26880) covalent geometry : angle 0.60938 / 0.31 (36601) hydrogen bonds : bond 0.05053 / 5.44 ( 1109) hydrogen bonds : angle 4.62779 / 5.20 ( 3051) metal coordination : bond 0.00578 / 0.51 ( 8) metal coordination : angle 4.41016 / 7.13 ( 12) *********************** 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 278 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 224 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8190 (tt0) REVERT: B 226 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8151 (mt-10) REVERT: C 121 GLU cc_start: 0.6554 (pt0) cc_final: 0.6146 (pp20) REVERT: C 183 TRP cc_start: 0.8552 (m-10) cc_final: 0.7967 (m-10) REVERT: C 195 PHE cc_start: 0.8510 (m-80) cc_final: 0.8185 (m-80) REVERT: C 284 LEU cc_start: 0.7644 (mt) cc_final: 0.7209 (tp) REVERT: C 315 MET cc_start: 0.7421 (mmm) cc_final: 0.7199 (mmm) REVERT: C 349 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7459 (tm-30) REVERT: C 434 ASP cc_start: 0.9046 (t0) cc_final: 0.8739 (t0) REVERT: C 484 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8428 (pt) REVERT: C 493 ILE cc_start: 0.8734 (pt) cc_final: 0.8520 (pt) REVERT: C 600 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8618 (p) REVERT: C 930 ASP cc_start: 0.8421 (t0) cc_final: 0.8044 (t0) REVERT: C 965 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7856 (tp-100) REVERT: C 1274 GLU cc_start: 0.8347 (mp0) cc_final: 0.8043 (mp0) REVERT: D 29 MET cc_start: 0.8380 (tpt) cc_final: 0.8080 (tmm) REVERT: D 91 GLU cc_start: 0.8067 (tt0) cc_final: 0.7346 (pp20) REVERT: D 235 GLU cc_start: 0.8917 (pm20) cc_final: 0.8650 (pm20) REVERT: D 330 MET cc_start: 0.8873 (ttm) cc_final: 0.8460 (ttm) REVERT: D 601 ILE cc_start: 0.8873 (tt) cc_final: 0.8610 (mt) REVERT: D 698 MET cc_start: 0.8259 (mmm) cc_final: 0.8050 (tpp) REVERT: D 699 ASP cc_start: 0.8353 (t0) cc_final: 0.8026 (m-30) REVERT: D 763 PHE cc_start: 0.9469 (OUTLIER) cc_final: 0.9000 (m-80) REVERT: D 822 MET cc_start: 0.8404 (mmm) cc_final: 0.7968 (mmm) REVERT: D 913 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 1095 MET cc_start: 0.5656 (ttt) cc_final: 0.5384 (tpp) REVERT: E 8 ASP cc_start: 0.8224 (p0) cc_final: 0.7643 (p0) REVERT: E 42 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8016 (mp0) REVERT: E 55 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: E 68 GLU cc_start: 0.8235 (tp30) cc_final: 0.7746 (tp30) REVERT: E 72 GLN cc_start: 0.9000 (tp40) cc_final: 0.8600 (mt0) outliers start: 54 outliers final: 26 residues processed: 270 average time/residue: 0.1582 time to fit residues: 71.6597 Evaluate side-chains 229 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 98 VAL 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 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 741 MET Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1253 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 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 763 PHE 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 55 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 195 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 274 optimal weight: 0.0030 chunk 254 optimal weight: 0.6980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN B 23 HIS C 688 GLN D 157 GLN D 777 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.118113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.082270 restraints weight = 55444.488| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.02 r_work: 0.3129 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26888 Z= 0.113 Angle : 0.596 25.789 36613 Z= 0.299 Chirality : 0.053 1.978 4185 Planarity : 0.004 0.045 4555 Dihedral : 14.576 179.093 4242 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.69 % Allowed : 12.12 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 3169 helix: 0.95 (0.16), residues: 1119 sheet: -0.62 (0.26), residues: 406 loop : -2.02 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1174 TYR 0.019 0.001 TYR D 679 PHE 0.022 0.001 PHE D 176 TRP 0.011 0.001 TRP C 997 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (26880) covalent geometry : angle 0.59313 / 0.30 (36601) hydrogen bonds : bond 0.04903 / 5.29 ( 1109) hydrogen bonds : angle 4.51495 / 5.09 ( 3051) metal coordination : bond 0.00481 / 0.42 ( 8) metal coordination : angle 3.46704 / 5.78 ( 12) *********************** 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 262 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 216 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.7937 (mp10) cc_final: 0.7592 (mp10) REVERT: B 226 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8182 (mt-10) REVERT: C 121 GLU cc_start: 0.6524 (pt0) cc_final: 0.6117 (pp20) REVERT: C 183 TRP cc_start: 0.8529 (m-10) cc_final: 0.7939 (m-10) REVERT: C 195 PHE cc_start: 0.8510 (m-80) cc_final: 0.8263 (m-80) REVERT: C 284 LEU cc_start: 0.7733 (mt) cc_final: 0.7291 (tp) REVERT: C 315 MET cc_start: 0.7513 (mmm) cc_final: 0.7273 (mmm) REVERT: C 349 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7429 (tm-30) REVERT: C 369 MET cc_start: 0.8680 (tmm) cc_final: 0.8283 (tmm) REVERT: C 434 ASP cc_start: 0.9044 (t0) cc_final: 0.8841 (t0) REVERT: C 484 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8443 (pt) REVERT: C 542 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7832 (mmp80) REVERT: C 600 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8538 (p) REVERT: C 930 ASP cc_start: 0.8474 (t0) cc_final: 0.8141 (t0) REVERT: C 946 LEU cc_start: 0.8735 (mp) cc_final: 0.8495 (mp) REVERT: C 965 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7866 (tp-100) REVERT: C 1274 GLU cc_start: 0.8367 (mp0) cc_final: 0.8057 (mp0) REVERT: C 1329 GLU cc_start: 0.8361 (tt0) cc_final: 0.8147 (tt0) REVERT: D 29 MET cc_start: 0.8402 (tpt) cc_final: 0.8064 (tmm) REVERT: D 91 GLU cc_start: 0.8080 (tt0) cc_final: 0.7366 (pp20) REVERT: D 151 MET cc_start: 0.8376 (ttm) cc_final: 0.8175 (ttt) REVERT: D 235 GLU cc_start: 0.8931 (pm20) cc_final: 0.8667 (pm20) REVERT: D 601 ILE cc_start: 0.8869 (tt) cc_final: 0.8584 (mt) REVERT: D 763 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.9043 (m-10) REVERT: D 822 MET cc_start: 0.8397 (mmm) cc_final: 0.7950 (mmm) REVERT: D 1095 MET cc_start: 0.5661 (ttt) cc_final: 0.5440 (tpp) REVERT: E 8 ASP cc_start: 0.8373 (p0) cc_final: 0.7804 (p0) REVERT: E 42 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8034 (mp0) REVERT: E 55 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: E 68 GLU cc_start: 0.8255 (tp30) cc_final: 0.7862 (tp30) REVERT: E 69 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7997 (tpm170) REVERT: E 72 GLN cc_start: 0.9063 (tp40) cc_final: 0.8542 (mt0) outliers start: 46 outliers final: 27 residues processed: 253 average time/residue: 0.1653 time to fit residues: 69.8998 Evaluate side-chains 231 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 199 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 98 VAL 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 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 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 1253 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 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 317 THR 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 624 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 763 PHE Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 69 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 41 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 208 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 232 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1146 GLN D 777 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.117036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.081654 restraints weight = 55721.237| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.99 r_work: 0.3096 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26888 Z= 0.143 Angle : 0.607 25.946 36613 Z= 0.304 Chirality : 0.053 1.984 4185 Planarity : 0.004 0.056 4555 Dihedral : 14.554 179.247 4242 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.69 % Allowed : 12.12 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.15), residues: 3169 helix: 1.01 (0.16), residues: 1120 sheet: -0.50 (0.26), residues: 411 loop : -1.96 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1173 TYR 0.017 0.001 TYR D 679 PHE 0.013 0.001 PHE D 620 TRP 0.006 0.001 TRP D 580 HIS 0.007 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (26880) covalent geometry : angle 0.60481 / 0.30 (36601) hydrogen bonds : bond 0.05033 / 5.45 ( 1109) hydrogen bonds : angle 4.47493 / 5.05 ( 3051) metal coordination : bond 0.00634 / 0.58 ( 8) metal coordination : angle 3.10355 / 5.43 ( 12) *********************** 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 248 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.7950 (mp10) cc_final: 0.7585 (mp10) REVERT: B 226 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8170 (mt-10) REVERT: C 121 GLU cc_start: 0.6606 (pt0) cc_final: 0.6373 (pp20) REVERT: C 183 TRP cc_start: 0.8563 (m-10) cc_final: 0.7965 (m-10) REVERT: C 195 PHE cc_start: 0.8526 (m-80) cc_final: 0.8275 (m-80) REVERT: C 284 LEU cc_start: 0.7758 (mt) cc_final: 0.7388 (tp) REVERT: C 315 MET cc_start: 0.7532 (mmm) cc_final: 0.7238 (mmm) REVERT: C 349 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7462 (tm-30) REVERT: C 484 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8452 (pt) REVERT: C 600 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8524 (p) REVERT: C 850 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7898 (mt) REVERT: C 930 ASP cc_start: 0.8462 (t0) cc_final: 0.8137 (t0) REVERT: C 965 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7797 (tp-100) REVERT: C 1085 MET cc_start: 0.9123 (mmp) cc_final: 0.8631 (mmt) REVERT: C 1274 GLU cc_start: 0.8377 (mp0) cc_final: 0.8069 (mp0) REVERT: D 29 MET cc_start: 0.8435 (tpt) cc_final: 0.8063 (tmm) REVERT: D 91 GLU cc_start: 0.8125 (tt0) cc_final: 0.7390 (pp20) REVERT: D 235 GLU cc_start: 0.8921 (pm20) cc_final: 0.8645 (pm20) REVERT: D 298 MET cc_start: 0.7897 (mmt) cc_final: 0.7545 (mtm) REVERT: D 763 PHE cc_start: 0.9458 (OUTLIER) cc_final: 0.9021 (m-10) REVERT: D 822 MET cc_start: 0.8390 (mmm) cc_final: 0.7922 (mmm) REVERT: D 1095 MET cc_start: 0.5575 (ttt) cc_final: 0.5345 (tpp) REVERT: E 8 ASP cc_start: 0.8449 (p0) cc_final: 0.7861 (p0) REVERT: E 42 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8072 (mp0) REVERT: E 55 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7463 (tp30) REVERT: E 69 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7993 (tpm170) outliers start: 46 outliers final: 33 residues processed: 241 average time/residue: 0.1649 time to fit residues: 66.3363 Evaluate side-chains 233 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 224 LEU Chi-restraints excluded: chain C residue 131 THR 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 600 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 317 THR 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 624 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 763 PHE 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 1261 LEU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 69 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 6 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 262 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN D 777 HIS D1195 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.115095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.078669 restraints weight = 56134.920| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.75 r_work: 0.3053 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26888 Z= 0.210 Angle : 0.676 25.977 36613 Z= 0.339 Chirality : 0.055 1.992 4185 Planarity : 0.004 0.055 4555 Dihedral : 14.580 178.452 4242 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.95 % Allowed : 12.67 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.15), residues: 3169 helix: 0.92 (0.16), residues: 1119 sheet: -0.64 (0.25), residues: 434 loop : -1.95 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1174 TYR 0.023 0.002 TYR D 631 PHE 0.024 0.002 PHE D 176 TRP 0.005 0.001 TRP D 686 HIS 0.008 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (26880) covalent geometry : angle 0.67357 / 0.34 (36601) hydrogen bonds : bond 0.05641 / 6.19 ( 1109) hydrogen bonds : angle 4.62853 / 5.21 ( 3051) metal coordination : bond 0.01004 / 0.98 ( 8) metal coordination : angle 2.97028 / 5.21 ( 12) *********************** 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 250 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8016 (mp10) cc_final: 0.7659 (mp10) REVERT: B 226 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8204 (mt-10) REVERT: C 121 GLU cc_start: 0.6925 (pt0) cc_final: 0.6426 (pp20) REVERT: C 132 ASP cc_start: 0.8587 (t0) cc_final: 0.8090 (t0) REVERT: C 284 LEU cc_start: 0.7814 (mt) cc_final: 0.7456 (tp) REVERT: C 315 MET cc_start: 0.7607 (mmm) cc_final: 0.7333 (mmm) REVERT: C 349 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7563 (tm-30) REVERT: C 484 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8541 (pt) REVERT: C 600 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 930 ASP cc_start: 0.8445 (t0) cc_final: 0.8011 (t0) REVERT: C 965 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7815 (tp-100) REVERT: D 91 GLU cc_start: 0.8227 (tt0) cc_final: 0.7537 (pp20) REVERT: D 235 GLU cc_start: 0.8928 (pm20) cc_final: 0.8662 (pm20) REVERT: D 698 MET cc_start: 0.8262 (mmm) cc_final: 0.7790 (tpp) REVERT: D 763 PHE cc_start: 0.9484 (OUTLIER) cc_final: 0.8980 (m-80) REVERT: D 1095 MET cc_start: 0.5540 (ttt) cc_final: 0.5273 (tpp) REVERT: D 1189 MET cc_start: 0.6721 (mtt) cc_final: 0.6397 (mtt) REVERT: E 8 ASP cc_start: 0.8412 (p0) cc_final: 0.8131 (p0) REVERT: E 42 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8075 (mp0) REVERT: E 62 GLN cc_start: 0.8530 (tp40) cc_final: 0.7566 (tm-30) REVERT: E 69 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8307 (tpm170) outliers start: 53 outliers final: 34 residues processed: 240 average time/residue: 0.1727 time to fit residues: 68.3976 Evaluate side-chains 223 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 183 ILE 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 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 727 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 949 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 317 THR 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 624 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 763 PHE 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 55 GLU Chi-restraints excluded: chain E residue 69 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 39 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 309 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN B 227 GLN C 65 ASN C 618 GLN D 777 HIS D1195 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.116317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.082263 restraints weight = 53325.836| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.72 r_work: 0.3062 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26888 Z= 0.121 Angle : 0.609 26.032 36613 Z= 0.306 Chirality : 0.053 1.989 4185 Planarity : 0.004 0.059 4555 Dihedral : 14.507 176.509 4242 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.77 % Allowed : 13.22 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3169 helix: 1.05 (0.16), residues: 1120 sheet: -0.43 (0.26), residues: 420 loop : -1.83 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 175 TYR 0.018 0.001 TYR D 679 PHE 0.010 0.001 PHE D 620 TRP 0.013 0.001 TRP C 183 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (26880) covalent geometry : angle 0.60720 / 0.31 (36601) hydrogen bonds : bond 0.05005 / 5.44 ( 1109) hydrogen bonds : angle 4.48550 / 5.04 ( 3051) metal coordination : bond 0.00498 / 0.47 ( 8) metal coordination : angle 2.54217 / 4.39 ( 12) *********************** 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 249 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.7977 (mp10) cc_final: 0.7639 (mp10) REVERT: B 226 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8177 (mt-10) REVERT: C 121 GLU cc_start: 0.6628 (pt0) cc_final: 0.6238 (pp20) REVERT: C 132 ASP cc_start: 0.8440 (t0) cc_final: 0.8116 (t0) REVERT: C 183 TRP cc_start: 0.8497 (m-10) cc_final: 0.8082 (m-10) REVERT: C 284 LEU cc_start: 0.7815 (mt) cc_final: 0.7465 (tp) REVERT: C 315 MET cc_start: 0.7490 (mmm) cc_final: 0.7168 (mmm) REVERT: C 349 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7507 (tm-30) REVERT: C 484 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8488 (pt) REVERT: C 600 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8472 (p) REVERT: C 876 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8006 (pp20) REVERT: C 930 ASP cc_start: 0.8365 (t0) cc_final: 0.8035 (t0) REVERT: C 965 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7721 (tp-100) REVERT: C 1160 ASP cc_start: 0.7844 (p0) cc_final: 0.7536 (p0) REVERT: D 29 MET cc_start: 0.8317 (tmm) cc_final: 0.7951 (tpp) REVERT: D 91 GLU cc_start: 0.8157 (tt0) cc_final: 0.7543 (pp20) REVERT: D 92 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7198 (m) REVERT: D 235 GLU cc_start: 0.8873 (pm20) cc_final: 0.8658 (pm20) REVERT: D 298 MET cc_start: 0.7811 (mmt) cc_final: 0.7571 (mtm) REVERT: D 601 ILE cc_start: 0.8985 (tt) cc_final: 0.8678 (mt) REVERT: D 698 MET cc_start: 0.8333 (mmm) cc_final: 0.8016 (tpp) REVERT: D 709 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7177 (ptm160) REVERT: D 763 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8987 (m-80) REVERT: D 1095 MET cc_start: 0.5534 (ttt) cc_final: 0.5283 (tpp) REVERT: D 1189 MET cc_start: 0.6724 (mtt) cc_final: 0.6442 (mtt) REVERT: E 8 ASP cc_start: 0.8385 (p0) cc_final: 0.8076 (p0) REVERT: E 42 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8090 (mp0) REVERT: E 69 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8104 (tpm170) outliers start: 48 outliers final: 33 residues processed: 241 average time/residue: 0.1685 time to fit residues: 67.5312 Evaluate side-chains 228 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 56 VAL 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 632 ASP 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 949 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 763 PHE 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 1261 LEU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 69 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 10 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 168 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS C 65 ASN D 777 HIS D1195 GLN ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.114932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.080665 restraints weight = 53397.716| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.71 r_work: 0.3027 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26888 Z= 0.178 Angle : 0.639 25.968 36613 Z= 0.320 Chirality : 0.054 1.989 4185 Planarity : 0.004 0.052 4555 Dihedral : 14.512 175.800 4242 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.92 % Allowed : 13.44 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3169 helix: 1.04 (0.16), residues: 1121 sheet: -0.44 (0.26), residues: 425 loop : -1.82 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 542 TYR 0.018 0.001 TYR D 631 PHE 0.021 0.001 PHE D 176 TRP 0.007 0.001 TRP D 33 HIS 0.007 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (26880) covalent geometry : angle 0.63716 / 0.32 (36601) hydrogen bonds : bond 0.05252 / 5.74 ( 1109) hydrogen bonds : angle 4.52541 / 5.08 ( 3051) metal coordination : bond 0.00816 / 0.79 ( 8) metal coordination : angle 2.52698 / 4.43 ( 12) ********************** 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 243 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 191 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 GLN cc_start: 0.8010 (mp10) cc_final: 0.7686 (mp10) REVERT: B 226 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8231 (mt-10) REVERT: C 121 GLU cc_start: 0.6749 (pt0) cc_final: 0.6300 (pp20) REVERT: C 132 ASP cc_start: 0.8519 (t0) cc_final: 0.8054 (t0) REVERT: C 183 TRP cc_start: 0.8568 (m-10) cc_final: 0.8138 (m-10) REVERT: C 284 LEU cc_start: 0.7806 (mt) cc_final: 0.7458 (tp) REVERT: C 315 MET cc_start: 0.7511 (mmm) cc_final: 0.7178 (mmm) REVERT: C 349 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 484 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8502 (pt) REVERT: C 600 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8468 (p) REVERT: C 876 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8020 (pp20) REVERT: C 930 ASP cc_start: 0.8373 (t0) cc_final: 0.8034 (t0) REVERT: C 965 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7745 (tp-100) REVERT: D 29 MET cc_start: 0.8311 (tmm) cc_final: 0.8086 (tpt) REVERT: D 91 GLU cc_start: 0.8172 (tt0) cc_final: 0.7464 (pp20) REVERT: D 235 GLU cc_start: 0.8898 (pm20) cc_final: 0.8675 (pm20) REVERT: D 698 MET cc_start: 0.8403 (mmm) cc_final: 0.8001 (tpp) REVERT: D 709 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7237 (ptm160) REVERT: D 763 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.8985 (m-80) REVERT: D 822 MET cc_start: 0.8166 (mmm) cc_final: 0.7778 (mmm) REVERT: D 1095 MET cc_start: 0.5598 (ttt) cc_final: 0.5328 (tpp) REVERT: D 1189 MET cc_start: 0.6684 (mtt) cc_final: 0.6429 (mtt) REVERT: E 8 ASP cc_start: 0.8378 (p0) cc_final: 0.8058 (p0) REVERT: E 42 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8091 (mp0) REVERT: E 69 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7979 (tpm170) outliers start: 52 outliers final: 39 residues processed: 233 average time/residue: 0.1594 time to fit residues: 62.6133 Evaluate side-chains 233 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 98 VAL 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 600 THR Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 949 GLU 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 1253 LEU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1327 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 317 THR 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 525 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 763 PHE 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 918 ILE Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain E residue 55 GLU Chi-restraints excluded: chain E residue 69 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 151 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 228 optimal weight: 0.0670 chunk 258 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 292 optimal weight: 8.9990 chunk 269 optimal weight: 7.9990 chunk 304 optimal weight: 0.8980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 ASN C 65 ASN D 777 HIS ** D1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.117183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.083440 restraints weight = 52739.304| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.74 r_work: 0.3069 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26888 Z= 0.116 Angle : 0.602 25.986 36613 Z= 0.302 Chirality : 0.053 1.988 4185 Planarity : 0.004 0.045 4555 Dihedral : 14.482 174.864 4242 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.69 % Allowed : 13.59 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.15), residues: 3169 helix: 1.16 (0.16), residues: 1119 sheet: -0.37 (0.26), residues: 419 loop : -1.71 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 542 TYR 0.018 0.001 TYR D 679 PHE 0.012 0.001 PHE D 620 TRP 0.009 0.001 TRP D 580 HIS 0.009 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (26880) covalent geometry : angle 0.60051 / 0.30 (36601) hydrogen bonds : bond 0.04827 / 5.25 ( 1109) hydrogen bonds : angle 4.40676 / 4.95 ( 3051) metal coordination : bond 0.00444 / 0.41 ( 8) metal coordination : angle 2.27399 / 4.00 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5994.07 seconds wall clock time: 103 minutes 31.01 seconds (6211.01 seconds total)