Starting phenix.real_space_refine on Thu Mar 5 20:32:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkp_23902/03_2026/7mkp_23902.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkp_23902/03_2026/7mkp_23902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mkp_23902/03_2026/7mkp_23902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkp_23902/03_2026/7mkp_23902.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkp_23902/03_2026/7mkp_23902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkp_23902/03_2026/7mkp_23902.cif" } resolution = 3.41 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= -0.001 sd= 0.030 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 105 5.16 5 C 15628 2.51 5 N 4407 2.21 5 O 4800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24943 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1794 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 9, 'TRANS': 221} Chain: "B" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1786 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 10432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1323, 10432 Classifications: {'peptide': 1323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1267} Chain breaks: 1 Chain: "D" Number of atoms: 10382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10382 Classifications: {'peptide': 1340} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 55, 'TRANS': 1284} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 546 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} 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 14477 SG CYS D 70 14.383 95.793 79.761 1.00593.33 S ATOM 14491 SG CYS D 72 12.984 98.729 78.032 1.00598.19 S ATOM 14599 SG CYS D 85 10.992 95.771 78.100 1.00613.35 S ATOM 14623 SG CYS D 88 14.067 95.973 76.026 1.00599.86 S ATOM 20311 SG CYS D 814 45.006 36.180 75.537 1.00147.26 S ATOM 20876 SG CYS D 888 46.650 39.566 75.164 1.00157.14 S ATOM 20927 SG CYS D 895 45.508 38.263 78.214 1.00144.69 S ATOM 20948 SG CYS D 898 48.205 36.865 77.068 1.00143.31 S Time building chain proxies: 4.88, per 1000 atoms: 0.20 Number of scatterers: 24943 At special positions: 0 Unit cell: (133.92, 164.16, 165.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 105 16.00 Mg 1 11.99 O 4800 8.00 N 4407 7.00 C 15628 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 814 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " Number of angles added : 12 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 44 sheets defined 39.1% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 4.150A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.871A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.576A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.004A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.824A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.626A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) 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 154 through 161 removed outlier: 4.056A pdb=" N ARG B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.766A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.626A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.517A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.670A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 242 through 247 removed outlier: 3.631A pdb=" N ARG C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.868A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 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 390 removed outlier: 3.817A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.577A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 482 removed outlier: 3.617A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.579A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.563A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.916A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 668 removed outlier: 3.816A pdb=" N ILE C 668 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 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 864 removed outlier: 3.664A pdb=" N LEU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 removed outlier: 3.776A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.708A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.609A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.618A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1101 through 1106' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.507A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1151 removed outlier: 3.549A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1166 through 1177 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.521A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.622A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.825A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1310 Processing helix chain 'C' and resid 1320 through 1332 Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 Processing helix chain 'D' and resid 113 through 119 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.792A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.801A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 309 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 388 Proline residue: D 379 - end of helix Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.502A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 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 504 through 515 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 Processing helix chain 'D' and resid 588 through 593 Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 636 removed outlier: 3.543A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.796A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.949A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 804 Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.657A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.814A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1147 removed outlier: 3.854A pdb=" N ARG D1140 " --> pdb=" O GLY D1136 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 4.024A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.701A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.553A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1324 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.548A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 4.000A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1373 removed outlier: 4.136A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 32 removed outlier: 3.517A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 70 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 8.662A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 8.013A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (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 111 removed outlier: 6.617A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.616A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 8.112A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.823A 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 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 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 13 through 14 removed outlier: 6.925A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.714A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.714A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.455A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'C' and resid 284 through 286 removed outlier: 4.247A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.774A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 6.082A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.740A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 749 through 752 removed outlier: 7.056A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.524A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.773A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 3.850A pdb=" N THR C 843 " --> pdb=" O GLY C 846 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP C 842 " --> pdb=" O VAL C1046 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL C1046 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.963A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1087 through 1088 Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.775A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.682A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.710A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 103 through 112 removed outlier: 10.156A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 144 through 146 removed outlier: 4.712A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 252 through 254 Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.180A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 991 through 997 removed outlier: 4.173A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR D 980 " --> pdb=" O VAL D 997 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.539A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE5, first strand: chain 'D' and resid 1035 through 1038 Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1061 removed outlier: 3.838A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1163 through 1165 removed outlier: 4.403A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1279 1067 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.35 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6205 1.33 - 1.45: 4374 1.45 - 1.57: 14548 1.57 - 1.69: 0 1.69 - 1.82: 182 Bond restraints: 25309 Sorted by residual: bond pdb=" N VAL C1159 " pdb=" CA VAL C1159 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.91e+00 bond pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.64e+00 bond pdb=" N PHE D 338 " pdb=" CA PHE D 338 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.60e+00 bond pdb=" N GLU C 940 " pdb=" CA GLU C 940 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.48e+00 bond pdb=" N ASP C1160 " pdb=" CA ASP C1160 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.43e+00 ... (remaining 25304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 33947 4.96 - 9.91: 210 9.91 - 14.87: 23 14.87 - 19.82: 2 19.82 - 24.78: 1 Bond angle restraints: 34183 Sorted by residual: angle pdb=" CA PRO D 758 " pdb=" N PRO D 758 " pdb=" CD PRO D 758 " ideal model delta sigma weight residual 112.00 101.09 10.91 1.40e+00 5.10e-01 6.07e+01 angle pdb=" CA LEU D 160 " pdb=" CB LEU D 160 " pdb=" CG LEU D 160 " ideal model delta sigma weight residual 116.30 141.08 -24.78 3.50e+00 8.16e-02 5.01e+01 angle pdb=" N GLU B 226 " pdb=" CA GLU B 226 " pdb=" CB GLU B 226 " ideal model delta sigma weight residual 110.16 120.00 -9.84 1.48e+00 4.57e-01 4.42e+01 angle pdb=" CA MET D 466 " pdb=" CB MET D 466 " pdb=" CG MET D 466 " ideal model delta sigma weight residual 114.10 126.55 -12.45 2.00e+00 2.50e-01 3.88e+01 angle pdb=" N GLU D 873 " pdb=" CA GLU D 873 " pdb=" CB GLU D 873 " ideal model delta sigma weight residual 110.16 119.10 -8.94 1.48e+00 4.57e-01 3.65e+01 ... (remaining 34178 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13998 17.98 - 35.97: 1296 35.97 - 53.95: 221 53.95 - 71.94: 61 71.94 - 89.92: 33 Dihedral angle restraints: 15609 sinusoidal: 6447 harmonic: 9162 Sorted by residual: dihedral pdb=" CA LYS C 236 " pdb=" C LYS C 236 " pdb=" N LEU C 237 " pdb=" CA LEU C 237 " ideal model delta harmonic sigma weight residual 180.00 138.79 41.21 0 5.00e+00 4.00e-02 6.79e+01 dihedral pdb=" CA THR C 595 " pdb=" C THR C 595 " pdb=" N ASP C 596 " pdb=" CA ASP C 596 " ideal model delta harmonic sigma weight residual 180.00 -143.03 -36.97 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CA ASP D1184 " pdb=" C ASP D1184 " pdb=" N PRO D1185 " pdb=" CA PRO D1185 " ideal model delta harmonic sigma weight residual 180.00 -144.97 -35.03 0 5.00e+00 4.00e-02 4.91e+01 ... (remaining 15606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3175 0.071 - 0.142: 609 0.142 - 0.214: 94 0.214 - 0.285: 16 0.285 - 0.356: 8 Chirality restraints: 3902 Sorted by residual: chirality pdb=" CG LEU C 538 " pdb=" CB LEU C 538 " pdb=" CD1 LEU C 538 " pdb=" CD2 LEU C 538 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CA LEU D 56 " pdb=" N LEU D 56 " pdb=" C LEU D 56 " pdb=" CB LEU D 56 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA GLU D1236 " pdb=" N GLU D1236 " pdb=" C GLU D1236 " pdb=" CB GLU D1236 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 3899 not shown) Planarity restraints: 4492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 757 " -0.141 5.00e-02 4.00e+02 2.05e-01 6.70e+01 pdb=" N PRO D 758 " 0.353 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.118 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 287 " 0.066 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO D 288 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 465 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CD GLN D 465 " 0.058 2.00e-02 2.50e+03 pdb=" OE1 GLN D 465 " -0.022 2.00e-02 2.50e+03 pdb=" NE2 GLN D 465 " -0.019 2.00e-02 2.50e+03 ... (remaining 4489 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 167 2.44 - 3.06: 17456 3.06 - 3.67: 38299 3.67 - 4.29: 53289 4.29 - 4.90: 87450 Nonbonded interactions: 196661 Sorted by model distance: nonbonded pdb=" OE2 GLU D 913 " pdb=" CE2 PHE E 17 " model vdw 1.831 3.340 nonbonded pdb=" N HIS C1313 " pdb=" OE1 GLN E 31 " model vdw 1.887 3.120 nonbonded pdb=" OD2 ASP D 464 " pdb="MG MG D2001 " model vdw 1.924 2.170 nonbonded pdb=" O LEU D1344 " pdb=" N GLY D1346 " model vdw 2.063 3.120 nonbonded pdb=" OG1 THR C 135 " pdb=" OE2 GLU C 142 " model vdw 2.074 3.040 ... (remaining 196656 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 235) selection = (chain 'B' and resid 7 through 235) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.280 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 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 : 0.006 0.376 25317 Z= 0.281 Angle : 1.094 24.777 34195 Z= 0.588 Chirality : 0.060 0.356 3902 Planarity : 0.007 0.205 4492 Dihedral : 14.847 89.919 9717 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.15 % Favored : 91.44 % Rotamer: Outliers : 0.81 % Allowed : 1.40 % Favored : 97.79 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.13 % 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: -2.49 (0.13), residues: 3177 helix: -0.65 (0.14), residues: 1100 sheet: -0.78 (0.25), residues: 378 loop : -2.64 (0.12), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG C 994 TYR 0.023 0.002 TYR D 772 PHE 0.053 0.002 PHE C 972 TRP 0.020 0.003 TRP C 997 HIS 0.024 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00547 (25309) covalent geometry : angle 1.09432 (34183) hydrogen bonds : bond 0.13667 ( 1060) hydrogen bonds : angle 6.64031 ( 3009) metal coordination : bond 0.17100 ( 8) metal coordination : angle 1.49016 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8733 (mppt) cc_final: 0.8511 (mppt) REVERT: C 106 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8728 (mt-10) REVERT: C 515 MET cc_start: 0.7623 (tpp) cc_final: 0.7409 (tpt) REVERT: C 704 MET cc_start: 0.8242 (mmp) cc_final: 0.7897 (mpp) REVERT: C 1023 HIS cc_start: 0.9017 (m90) cc_final: 0.8681 (m90) REVERT: C 1315 MET cc_start: 0.7611 (tmm) cc_final: 0.7308 (tmm) REVERT: D 53 ARG cc_start: 0.8877 (mmp-170) cc_final: 0.8202 (mmp-170) REVERT: D 102 MET cc_start: 0.9147 (mmm) cc_final: 0.8885 (tmm) REVERT: D 298 MET cc_start: 0.9103 (mmp) cc_final: 0.8871 (mmp) REVERT: D 343 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8251 (mt) REVERT: D 345 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8451 (mttp) REVERT: D 458 ASN cc_start: 0.9195 (t0) cc_final: 0.8787 (t0) REVERT: D 907 HIS cc_start: 0.8377 (m90) cc_final: 0.7975 (m90) outliers start: 22 outliers final: 2 residues processed: 206 average time/residue: 0.1643 time to fit residues: 53.9767 Evaluate side-chains 142 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 345 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 41 ASN B 147 GLN C 46 GLN C 235 ASN C 618 GLN C 761 GLN ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 266 ASN D 277 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 771 GLN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.078621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052412 restraints weight = 126637.287| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 5.74 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25317 Z= 0.231 Angle : 0.779 13.110 34195 Z= 0.400 Chirality : 0.046 0.230 3902 Planarity : 0.006 0.093 4492 Dihedral : 5.945 58.204 3514 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 0.92 % Allowed : 9.63 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -1.24 (0.14), residues: 3177 helix: 0.60 (0.15), residues: 1102 sheet: -0.33 (0.25), residues: 382 loop : -1.99 (0.13), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.022 0.002 TYR D 772 PHE 0.023 0.002 PHE D 141 TRP 0.019 0.002 TRP D 33 HIS 0.009 0.002 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00527 (25309) covalent geometry : angle 0.77647 (34183) hydrogen bonds : bond 0.04960 ( 1060) hydrogen bonds : angle 5.35843 ( 3009) metal coordination : bond 0.00838 ( 8) metal coordination : angle 3.29924 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 GLU cc_start: 0.8653 (mp0) cc_final: 0.8433 (mp0) REVERT: C 47 TYR cc_start: 0.8127 (m-80) cc_final: 0.7463 (m-80) REVERT: C 106 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8885 (mt-10) REVERT: C 290 GLU cc_start: 0.9553 (mm-30) cc_final: 0.9191 (pp20) REVERT: C 369 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8177 (tpt) REVERT: C 515 MET cc_start: 0.7949 (tpp) cc_final: 0.7694 (tpt) REVERT: C 741 MET cc_start: 0.7511 (tpt) cc_final: 0.7278 (tpp) REVERT: C 936 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.5210 (ttp80) REVERT: C 1023 HIS cc_start: 0.9210 (m90) cc_final: 0.8565 (m90) REVERT: C 1027 LYS cc_start: 0.9322 (ptpp) cc_final: 0.9110 (ptpt) REVERT: C 1274 GLU cc_start: 0.8580 (mp0) cc_final: 0.8370 (mp0) REVERT: C 1315 MET cc_start: 0.7257 (tmm) cc_final: 0.7025 (tmm) REVERT: D 53 ARG cc_start: 0.8919 (mmp-170) cc_final: 0.8188 (mmp-170) REVERT: D 180 MET cc_start: 0.3106 (mmm) cc_final: 0.1979 (mmt) REVERT: D 345 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8824 (mmtm) REVERT: D 458 ASN cc_start: 0.9378 (t0) cc_final: 0.9090 (t0) REVERT: D 466 MET cc_start: 0.8518 (tpt) cc_final: 0.8206 (tpt) REVERT: D 743 MET cc_start: 0.8533 (mtm) cc_final: 0.8331 (mtm) REVERT: D 872 LEU cc_start: 0.9297 (mt) cc_final: 0.9078 (mt) REVERT: D 907 HIS cc_start: 0.8623 (m90) cc_final: 0.8088 (m-70) REVERT: D 915 ILE cc_start: 0.9478 (pt) cc_final: 0.9079 (mt) REVERT: D 1244 GLN cc_start: 0.9317 (mm110) cc_final: 0.8867 (mp10) outliers start: 25 outliers final: 11 residues processed: 175 average time/residue: 0.1634 time to fit residues: 46.2548 Evaluate side-chains 145 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 1162 SER Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 345 LYS Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 1035 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 39 optimal weight: 5.9990 chunk 312 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 chunk 237 optimal weight: 0.7980 chunk 210 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 291 optimal weight: 5.9990 chunk 252 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 235 ASN C 618 GLN C 808 ASN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN D 875 ASN ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.079926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053834 restraints weight = 126131.640| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 5.80 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25317 Z= 0.124 Angle : 0.650 9.573 34195 Z= 0.332 Chirality : 0.043 0.239 3902 Planarity : 0.005 0.058 4492 Dihedral : 5.372 55.828 3512 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 1.29 % Allowed : 12.18 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.71 (0.14), residues: 3177 helix: 1.02 (0.15), residues: 1105 sheet: 0.08 (0.25), residues: 382 loop : -1.69 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 99 TYR 0.015 0.001 TYR D 795 PHE 0.015 0.001 PHE C1270 TRP 0.021 0.001 TRP D1193 HIS 0.007 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00274 (25309) covalent geometry : angle 0.64875 (34183) hydrogen bonds : bond 0.04094 ( 1060) hydrogen bonds : angle 4.81891 ( 3009) metal coordination : bond 0.00529 ( 8) metal coordination : angle 2.26247 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 199 ASP cc_start: 0.8616 (p0) cc_final: 0.8135 (t70) REVERT: C 106 GLU cc_start: 0.9255 (OUTLIER) cc_final: 0.8789 (mt-10) REVERT: C 142 GLU cc_start: 0.8324 (tp30) cc_final: 0.7971 (tp30) REVERT: C 681 MET cc_start: 0.8457 (ptp) cc_final: 0.7866 (ptp) REVERT: C 741 MET cc_start: 0.7634 (tpt) cc_final: 0.7310 (tpp) REVERT: C 936 ARG cc_start: 0.6781 (OUTLIER) cc_final: 0.5157 (ttp80) REVERT: C 1023 HIS cc_start: 0.9254 (m90) cc_final: 0.8597 (m90) REVERT: C 1085 MET cc_start: 0.9293 (mmm) cc_final: 0.8737 (mmm) REVERT: C 1274 GLU cc_start: 0.8687 (mp0) cc_final: 0.8443 (mp0) REVERT: D 53 ARG cc_start: 0.8986 (mmp-170) cc_final: 0.8323 (mmp-170) REVERT: D 68 TYR cc_start: 0.8421 (m-10) cc_final: 0.8142 (m-80) REVERT: D 102 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7445 (tpp) REVERT: D 180 MET cc_start: 0.3372 (mmm) cc_final: 0.2239 (mmt) REVERT: D 298 MET cc_start: 0.8885 (mmp) cc_final: 0.8626 (mmp) REVERT: D 301 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9187 (tp30) REVERT: D 400 MET cc_start: 0.9393 (ttt) cc_final: 0.9138 (ptp) REVERT: D 413 ASP cc_start: 0.9292 (t70) cc_final: 0.8793 (t0) REVERT: D 458 ASN cc_start: 0.9325 (t0) cc_final: 0.9039 (t0) REVERT: D 466 MET cc_start: 0.8525 (tpt) cc_final: 0.8196 (tpt) REVERT: D 907 HIS cc_start: 0.8585 (m90) cc_final: 0.8036 (m-70) REVERT: E 30 MET cc_start: 0.6667 (mmp) cc_final: 0.6439 (mmt) outliers start: 35 outliers final: 17 residues processed: 187 average time/residue: 0.1491 time to fit residues: 46.5597 Evaluate side-chains 162 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 59 optimal weight: 0.9990 chunk 235 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 62 optimal weight: 0.0050 chunk 152 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN C 165 HIS ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.080384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054458 restraints weight = 125229.086| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 5.79 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 25317 Z= 0.110 Angle : 0.621 8.822 34195 Z= 0.314 Chirality : 0.042 0.234 3902 Planarity : 0.004 0.055 4492 Dihedral : 5.002 53.567 3508 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 2.25 % Allowed : 13.40 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.45 (0.14), residues: 3177 helix: 1.19 (0.16), residues: 1108 sheet: 0.44 (0.26), residues: 367 loop : -1.56 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 99 TYR 0.012 0.001 TYR C 742 PHE 0.023 0.001 PHE C1025 TRP 0.025 0.001 TRP D1193 HIS 0.006 0.001 HIS C1244 Details of bonding type rmsd covalent geometry : bond 0.00241 (25309) covalent geometry : angle 0.62033 (34183) hydrogen bonds : bond 0.03709 ( 1060) hydrogen bonds : angle 4.63085 ( 3009) metal coordination : bond 0.00335 ( 8) metal coordination : angle 1.92608 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 160 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.8623 (p0) cc_final: 0.8212 (t70) REVERT: C 142 GLU cc_start: 0.8340 (tp30) cc_final: 0.7973 (tp30) REVERT: C 741 MET cc_start: 0.7528 (tpt) cc_final: 0.7182 (tpp) REVERT: C 936 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.5117 (ttp80) REVERT: C 1023 HIS cc_start: 0.9256 (m90) cc_final: 0.8672 (m90) REVERT: C 1274 GLU cc_start: 0.8706 (mp0) cc_final: 0.8432 (mp0) REVERT: D 53 ARG cc_start: 0.8977 (mmp-170) cc_final: 0.8677 (mmp-170) REVERT: D 68 TYR cc_start: 0.8430 (m-10) cc_final: 0.8138 (m-80) REVERT: D 102 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7351 (tpp) REVERT: D 180 MET cc_start: 0.3244 (mmm) cc_final: 0.2983 (mmp) REVERT: D 298 MET cc_start: 0.8910 (mmp) cc_final: 0.8638 (mmp) REVERT: D 330 MET cc_start: 0.8572 (tmm) cc_final: 0.8261 (ppp) REVERT: D 400 MET cc_start: 0.9412 (ttt) cc_final: 0.9160 (ptp) REVERT: D 413 ASP cc_start: 0.9304 (t70) cc_final: 0.8849 (t0) REVERT: D 458 ASN cc_start: 0.9331 (t0) cc_final: 0.9054 (t0) REVERT: D 466 MET cc_start: 0.8513 (tpt) cc_final: 0.8192 (tpt) REVERT: D 724 MET cc_start: 0.8389 (mtt) cc_final: 0.8036 (mmt) REVERT: D 907 HIS cc_start: 0.8556 (m90) cc_final: 0.8001 (m-70) REVERT: D 1189 MET cc_start: 0.9238 (mmm) cc_final: 0.8825 (tpp) REVERT: E 30 MET cc_start: 0.6688 (mmp) cc_final: 0.6455 (mmt) outliers start: 61 outliers final: 24 residues processed: 210 average time/residue: 0.1396 time to fit residues: 49.4413 Evaluate side-chains 167 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 271 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 227 GLN C 618 GLN C1236 ASN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.079136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.053195 restraints weight = 126100.542| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 5.81 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25317 Z= 0.138 Angle : 0.624 9.498 34195 Z= 0.314 Chirality : 0.042 0.228 3902 Planarity : 0.004 0.058 4492 Dihedral : 4.734 43.341 3502 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.45 % Favored : 94.52 % Rotamer: Outliers : 1.88 % Allowed : 14.95 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.34 (0.15), residues: 3177 helix: 1.22 (0.16), residues: 1110 sheet: 0.41 (0.26), residues: 380 loop : -1.42 (0.14), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 994 TYR 0.035 0.001 TYR C 62 PHE 0.021 0.001 PHE C1025 TRP 0.023 0.001 TRP D1193 HIS 0.005 0.001 HIS C1244 Details of bonding type rmsd covalent geometry : bond 0.00312 (25309) covalent geometry : angle 0.62322 (34183) hydrogen bonds : bond 0.03811 ( 1060) hydrogen bonds : angle 4.58300 ( 3009) metal coordination : bond 0.00517 ( 8) metal coordination : angle 1.87819 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 147 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: A 199 ASP cc_start: 0.8691 (p0) cc_final: 0.8182 (t0) REVERT: C 142 GLU cc_start: 0.8570 (tp30) cc_final: 0.8240 (mm-30) REVERT: C 741 MET cc_start: 0.7659 (tpt) cc_final: 0.7311 (tpp) REVERT: C 1023 HIS cc_start: 0.9316 (m90) cc_final: 0.8760 (m90) REVERT: C 1274 GLU cc_start: 0.8705 (mp0) cc_final: 0.8441 (mt-10) REVERT: D 53 ARG cc_start: 0.8996 (mmp-170) cc_final: 0.8702 (mmp-170) REVERT: D 68 TYR cc_start: 0.8448 (m-10) cc_final: 0.8168 (m-80) REVERT: D 102 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7332 (tpp) REVERT: D 180 MET cc_start: 0.3401 (mmm) cc_final: 0.2514 (mmt) REVERT: D 298 MET cc_start: 0.8925 (mmp) cc_final: 0.8553 (mmp) REVERT: D 301 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9175 (tp30) REVERT: D 400 MET cc_start: 0.9401 (ttt) cc_final: 0.9172 (ptp) REVERT: D 413 ASP cc_start: 0.9372 (t70) cc_final: 0.8919 (t0) REVERT: D 458 ASN cc_start: 0.9330 (t0) cc_final: 0.9044 (t0) REVERT: D 466 MET cc_start: 0.8539 (tpt) cc_final: 0.8203 (tpt) REVERT: D 725 MET cc_start: 0.9182 (mtm) cc_final: 0.8973 (mtm) REVERT: D 907 HIS cc_start: 0.8556 (m90) cc_final: 0.7988 (m90) REVERT: D 1080 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8075 (tp) REVERT: D 1189 MET cc_start: 0.9327 (mmm) cc_final: 0.8921 (tpp) REVERT: E 30 MET cc_start: 0.6939 (mmp) cc_final: 0.6735 (mmt) outliers start: 51 outliers final: 28 residues processed: 187 average time/residue: 0.1472 time to fit residues: 46.0886 Evaluate side-chains 169 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 220 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 203 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 221 optimal weight: 1.9990 chunk 286 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1009 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.077371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.051156 restraints weight = 125657.957| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.67 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 25317 Z= 0.205 Angle : 0.675 12.922 34195 Z= 0.341 Chirality : 0.043 0.221 3902 Planarity : 0.005 0.057 4492 Dihedral : 4.833 33.558 3498 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer: Outliers : 2.14 % Allowed : 15.58 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.39 (0.15), residues: 3177 helix: 1.09 (0.16), residues: 1119 sheet: 0.22 (0.25), residues: 402 loop : -1.37 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 994 TYR 0.021 0.002 TYR C 62 PHE 0.023 0.002 PHE C1025 TRP 0.023 0.002 TRP D1193 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00461 (25309) covalent geometry : angle 0.67469 (34183) hydrogen bonds : bond 0.04324 ( 1060) hydrogen bonds : angle 4.75074 ( 3009) metal coordination : bond 0.00851 ( 8) metal coordination : angle 1.85504 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 142 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8551 (pm20) REVERT: C 142 GLU cc_start: 0.8719 (tp30) cc_final: 0.8406 (mm-30) REVERT: C 290 GLU cc_start: 0.9526 (mm-30) cc_final: 0.9128 (pp20) REVERT: C 1023 HIS cc_start: 0.9308 (m90) cc_final: 0.8831 (m90) REVERT: C 1095 ASP cc_start: 0.8580 (t0) cc_final: 0.8377 (t0) REVERT: D 53 ARG cc_start: 0.8948 (mmp-170) cc_final: 0.8641 (mmp-170) REVERT: D 140 TYR cc_start: 0.8882 (m-10) cc_final: 0.8541 (m-10) REVERT: D 298 MET cc_start: 0.8940 (mmp) cc_final: 0.8718 (mmp) REVERT: D 301 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.9149 (tp30) REVERT: D 458 ASN cc_start: 0.9356 (t0) cc_final: 0.9087 (t0) REVERT: D 466 MET cc_start: 0.8491 (tpt) cc_final: 0.8137 (tpt) REVERT: D 907 HIS cc_start: 0.8450 (m90) cc_final: 0.7911 (m90) REVERT: D 1080 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8126 (tp) REVERT: D 1189 MET cc_start: 0.9288 (mmm) cc_final: 0.9055 (mmm) REVERT: E 30 MET cc_start: 0.7222 (mmp) cc_final: 0.7015 (mmt) outliers start: 58 outliers final: 34 residues processed: 190 average time/residue: 0.1498 time to fit residues: 47.1490 Evaluate side-chains 165 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Chi-restraints excluded: chain D residue 1370 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 229 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 221 optimal weight: 0.3980 chunk 29 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1236 ASN D 340 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.078280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.052401 restraints weight = 125017.704| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.64 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25317 Z= 0.132 Angle : 0.639 10.851 34195 Z= 0.321 Chirality : 0.042 0.220 3902 Planarity : 0.004 0.057 4492 Dihedral : 4.660 32.212 3498 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.32 % Favored : 94.62 % Rotamer: Outliers : 1.85 % Allowed : 16.35 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.31 (0.15), residues: 3177 helix: 1.14 (0.16), residues: 1121 sheet: 0.30 (0.26), residues: 394 loop : -1.32 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 47 TYR 0.018 0.001 TYR C 62 PHE 0.025 0.001 PHE C1025 TRP 0.037 0.002 TRP D1193 HIS 0.006 0.001 HIS C1244 Details of bonding type rmsd covalent geometry : bond 0.00298 (25309) covalent geometry : angle 0.63876 (34183) hydrogen bonds : bond 0.03926 ( 1060) hydrogen bonds : angle 4.62457 ( 3009) metal coordination : bond 0.00466 ( 8) metal coordination : angle 1.56454 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 141 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: A 199 ASP cc_start: 0.8685 (p0) cc_final: 0.8165 (t70) REVERT: C 142 GLU cc_start: 0.8782 (tp30) cc_final: 0.8394 (mm-30) REVERT: C 653 MET cc_start: 0.8346 (tmm) cc_final: 0.8129 (tmm) REVERT: C 741 MET cc_start: 0.7723 (tpp) cc_final: 0.7522 (tpp) REVERT: C 1023 HIS cc_start: 0.9362 (m90) cc_final: 0.8927 (m90) REVERT: D 53 ARG cc_start: 0.8961 (mmp-170) cc_final: 0.8728 (mmp-170) REVERT: D 102 MET cc_start: 0.8307 (tpt) cc_final: 0.7314 (tpp) REVERT: D 140 TYR cc_start: 0.8902 (m-10) cc_final: 0.8543 (m-10) REVERT: D 180 MET cc_start: 0.3877 (mmm) cc_final: 0.2570 (mmt) REVERT: D 298 MET cc_start: 0.8936 (mmp) cc_final: 0.8551 (mmp) REVERT: D 301 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.9170 (tp30) REVERT: D 413 ASP cc_start: 0.9386 (t70) cc_final: 0.9011 (t0) REVERT: D 458 ASN cc_start: 0.9344 (t0) cc_final: 0.9039 (t0) REVERT: D 466 MET cc_start: 0.8569 (tpt) cc_final: 0.8169 (tpt) REVERT: D 581 MET cc_start: 0.9019 (tpp) cc_final: 0.8772 (mmt) REVERT: D 724 MET cc_start: 0.8464 (mtt) cc_final: 0.8215 (mmt) REVERT: D 743 MET cc_start: 0.8041 (mtt) cc_final: 0.7557 (mmm) REVERT: D 907 HIS cc_start: 0.8456 (m90) cc_final: 0.7888 (m90) REVERT: D 1080 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8089 (tp) REVERT: D 1189 MET cc_start: 0.9339 (mmm) cc_final: 0.9062 (mmm) REVERT: D 1260 MET cc_start: 0.9104 (ttt) cc_final: 0.8892 (ttm) REVERT: E 30 MET cc_start: 0.7301 (mmp) cc_final: 0.7097 (mmt) outliers start: 50 outliers final: 34 residues processed: 183 average time/residue: 0.1398 time to fit residues: 42.9318 Evaluate side-chains 171 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 312 optimal weight: 5.9990 chunk 6 optimal weight: 0.3980 chunk 114 optimal weight: 0.0020 chunk 175 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.078149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.052139 restraints weight = 125120.483| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.66 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25317 Z= 0.134 Angle : 0.638 11.610 34195 Z= 0.319 Chirality : 0.042 0.215 3902 Planarity : 0.004 0.057 4492 Dihedral : 4.594 31.737 3498 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 2.14 % Allowed : 16.65 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.24 (0.15), residues: 3177 helix: 1.24 (0.16), residues: 1116 sheet: 0.25 (0.25), residues: 410 loop : -1.29 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 994 TYR 0.022 0.001 TYR C 62 PHE 0.023 0.001 PHE C1025 TRP 0.038 0.002 TRP D1193 HIS 0.006 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00304 (25309) covalent geometry : angle 0.63780 (34183) hydrogen bonds : bond 0.03848 ( 1060) hydrogen bonds : angle 4.57714 ( 3009) metal coordination : bond 0.00494 ( 8) metal coordination : angle 1.57349 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8589 (pm20) REVERT: A 199 ASP cc_start: 0.8694 (p0) cc_final: 0.8184 (t70) REVERT: B 25 LYS cc_start: 0.9220 (mmmm) cc_final: 0.9000 (mmmm) REVERT: C 142 GLU cc_start: 0.8832 (tp30) cc_final: 0.8502 (mm-30) REVERT: C 369 MET cc_start: 0.7726 (mtt) cc_final: 0.7495 (mtp) REVERT: C 403 MET cc_start: 0.9169 (ppp) cc_final: 0.8748 (ppp) REVERT: C 741 MET cc_start: 0.7796 (tpp) cc_final: 0.7569 (tpp) REVERT: C 1023 HIS cc_start: 0.9342 (m90) cc_final: 0.8901 (m90) REVERT: C 1232 MET cc_start: 0.8404 (mmm) cc_final: 0.8137 (mmm) REVERT: D 53 ARG cc_start: 0.8971 (mmp-170) cc_final: 0.8747 (mmp-170) REVERT: D 102 MET cc_start: 0.8246 (tpt) cc_final: 0.7234 (tpp) REVERT: D 140 TYR cc_start: 0.8900 (m-10) cc_final: 0.8512 (m-10) REVERT: D 180 MET cc_start: 0.3864 (mmm) cc_final: 0.2657 (mmt) REVERT: D 298 MET cc_start: 0.8932 (mmp) cc_final: 0.8525 (mmp) REVERT: D 301 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.9144 (tp30) REVERT: D 330 MET cc_start: 0.8612 (ppp) cc_final: 0.8398 (ppp) REVERT: D 400 MET cc_start: 0.9387 (ttt) cc_final: 0.9133 (ptm) REVERT: D 413 ASP cc_start: 0.9369 (t70) cc_final: 0.8980 (t0) REVERT: D 458 ASN cc_start: 0.9341 (t0) cc_final: 0.9027 (t0) REVERT: D 466 MET cc_start: 0.8575 (tpt) cc_final: 0.8239 (tpt) REVERT: D 581 MET cc_start: 0.9004 (tpp) cc_final: 0.8729 (mmt) REVERT: D 724 MET cc_start: 0.8477 (mtt) cc_final: 0.8037 (mmt) REVERT: D 743 MET cc_start: 0.8096 (mtt) cc_final: 0.7549 (mmm) REVERT: D 907 HIS cc_start: 0.8420 (m90) cc_final: 0.7848 (m90) REVERT: D 1080 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8135 (tp) REVERT: D 1260 MET cc_start: 0.9066 (ttt) cc_final: 0.8845 (ttm) REVERT: D 1273 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8376 (t70) outliers start: 58 outliers final: 45 residues processed: 188 average time/residue: 0.1463 time to fit residues: 46.1499 Evaluate side-chains 186 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 137 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 273 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 310 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 101 optimal weight: 0.1980 chunk 308 optimal weight: 10.0000 chunk 173 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.077131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.051014 restraints weight = 125556.758| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 5.81 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25317 Z= 0.172 Angle : 0.662 11.100 34195 Z= 0.332 Chirality : 0.042 0.210 3902 Planarity : 0.004 0.056 4492 Dihedral : 4.711 32.249 3498 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.11 % Rotamer: Outliers : 2.29 % Allowed : 16.43 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.26 (0.15), residues: 3177 helix: 1.20 (0.16), residues: 1120 sheet: 0.18 (0.25), residues: 410 loop : -1.27 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 994 TYR 0.023 0.001 TYR A 177 PHE 0.024 0.001 PHE C1025 TRP 0.033 0.002 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00389 (25309) covalent geometry : angle 0.66154 (34183) hydrogen bonds : bond 0.04108 ( 1060) hydrogen bonds : angle 4.67884 ( 3009) metal coordination : bond 0.00696 ( 8) metal coordination : angle 1.67993 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 133 time to evaluate : 0.999 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 194 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: C 142 GLU cc_start: 0.8834 (tp30) cc_final: 0.8402 (mm-30) REVERT: C 741 MET cc_start: 0.7841 (tpp) cc_final: 0.7630 (tpp) REVERT: C 1023 HIS cc_start: 0.9390 (m90) cc_final: 0.8978 (m90) REVERT: D 140 TYR cc_start: 0.8973 (m-10) cc_final: 0.8726 (m-10) REVERT: D 180 MET cc_start: 0.3960 (mmm) cc_final: 0.3067 (mmt) REVERT: D 298 MET cc_start: 0.8945 (mmp) cc_final: 0.8543 (mmp) REVERT: D 301 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9143 (tp30) REVERT: D 330 MET cc_start: 0.8669 (ppp) cc_final: 0.8454 (ppp) REVERT: D 400 MET cc_start: 0.9330 (ttt) cc_final: 0.9082 (ptm) REVERT: D 458 ASN cc_start: 0.9332 (t0) cc_final: 0.9033 (t0) REVERT: D 466 MET cc_start: 0.8548 (tpt) cc_final: 0.8174 (tpt) REVERT: D 484 MET cc_start: 0.9019 (pmm) cc_final: 0.8733 (pmm) REVERT: D 724 MET cc_start: 0.8501 (mtt) cc_final: 0.8167 (mmt) REVERT: D 795 TYR cc_start: 0.9046 (t80) cc_final: 0.8814 (t80) REVERT: D 1080 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8046 (tp) REVERT: D 1260 MET cc_start: 0.9082 (ttt) cc_final: 0.8871 (ttm) REVERT: D 1273 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8358 (t70) outliers start: 62 outliers final: 47 residues processed: 183 average time/residue: 0.1406 time to fit residues: 43.6970 Evaluate side-chains 182 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 131 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 903 LEU Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 199 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 298 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 174 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1236 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.077591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.051644 restraints weight = 125496.268| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 5.70 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25317 Z= 0.145 Angle : 0.661 10.637 34195 Z= 0.330 Chirality : 0.042 0.208 3902 Planarity : 0.004 0.057 4492 Dihedral : 4.661 32.873 3498 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 1.96 % Allowed : 16.94 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.20 (0.15), residues: 3177 helix: 1.23 (0.16), residues: 1119 sheet: 0.20 (0.25), residues: 410 loop : -1.22 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 936 TYR 0.021 0.001 TYR A 177 PHE 0.024 0.001 PHE C1025 TRP 0.031 0.002 TRP D1193 HIS 0.006 0.001 HIS C 551 Details of bonding type rmsd covalent geometry : bond 0.00329 (25309) covalent geometry : angle 0.66083 (34183) hydrogen bonds : bond 0.03947 ( 1060) hydrogen bonds : angle 4.65007 ( 3009) metal coordination : bond 0.00537 ( 8) metal coordination : angle 1.54164 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6354 Ramachandran restraints generated. 3177 Oldfield, 0 Emsley, 3177 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: C 142 GLU cc_start: 0.8771 (tp30) cc_final: 0.8324 (mm-30) REVERT: C 370 MET cc_start: 0.9256 (mpp) cc_final: 0.9053 (pmm) REVERT: C 403 MET cc_start: 0.9098 (ppp) cc_final: 0.8651 (ppp) REVERT: C 685 MET cc_start: 0.8847 (ptp) cc_final: 0.8583 (ptp) REVERT: C 741 MET cc_start: 0.7796 (tpp) cc_final: 0.7586 (tpp) REVERT: C 1023 HIS cc_start: 0.9368 (m90) cc_final: 0.8952 (m90) REVERT: C 1232 MET cc_start: 0.8381 (mmm) cc_final: 0.7896 (mmm) REVERT: C 1304 MET cc_start: 0.9077 (tpt) cc_final: 0.8775 (tpp) REVERT: D 102 MET cc_start: 0.8212 (tpt) cc_final: 0.7246 (tpp) REVERT: D 140 TYR cc_start: 0.8991 (m-10) cc_final: 0.8726 (m-10) REVERT: D 180 MET cc_start: 0.3670 (mmm) cc_final: 0.2921 (mmt) REVERT: D 298 MET cc_start: 0.8942 (mmp) cc_final: 0.8542 (mmp) REVERT: D 301 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9150 (tp30) REVERT: D 330 MET cc_start: 0.8714 (ppp) cc_final: 0.8503 (ppp) REVERT: D 400 MET cc_start: 0.9322 (ttt) cc_final: 0.9117 (ptm) REVERT: D 458 ASN cc_start: 0.9321 (t0) cc_final: 0.9061 (t0) REVERT: D 466 MET cc_start: 0.8501 (tpt) cc_final: 0.8201 (tpt) REVERT: D 484 MET cc_start: 0.8926 (pmm) cc_final: 0.8642 (pmm) REVERT: D 581 MET cc_start: 0.9006 (tpp) cc_final: 0.8713 (mmt) REVERT: D 724 MET cc_start: 0.8451 (mtt) cc_final: 0.8104 (mmt) REVERT: D 743 MET cc_start: 0.7881 (mtt) cc_final: 0.7446 (mmm) REVERT: D 795 TYR cc_start: 0.9046 (t80) cc_final: 0.8810 (t80) REVERT: D 1080 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.7958 (tp) REVERT: D 1189 MET cc_start: 0.9334 (mmm) cc_final: 0.9074 (tpp) REVERT: D 1260 MET cc_start: 0.9057 (ttt) cc_final: 0.8851 (ttm) outliers start: 53 outliers final: 45 residues processed: 182 average time/residue: 0.1432 time to fit residues: 43.9781 Evaluate side-chains 180 residues out of total 2717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 194 GLN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 828 PHE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 968 GLU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 625 MET Chi-restraints excluded: chain D residue 639 VAL Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 966 VAL Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1035 VAL Chi-restraints excluded: chain D residue 1080 ILE Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1236 GLU Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 HIS C 437 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.076836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050606 restraints weight = 126614.747| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 5.95 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25317 Z= 0.175 Angle : 0.677 10.186 34195 Z= 0.340 Chirality : 0.043 0.203 3902 Planarity : 0.004 0.056 4492 Dihedral : 4.745 36.109 3498 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.11 % Rotamer: Outliers : 1.96 % Allowed : 17.17 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.77 % 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: -0.21 (0.15), residues: 3177 helix: 1.18 (0.16), residues: 1118 sheet: 0.08 (0.25), residues: 428 loop : -1.17 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 994 TYR 0.022 0.001 TYR A 177 PHE 0.025 0.001 PHE C1025 TRP 0.030 0.002 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd covalent geometry : bond 0.00396 (25309) covalent geometry : angle 0.67609 (34183) hydrogen bonds : bond 0.04144 ( 1060) hydrogen bonds : angle 4.73487 ( 3009) metal coordination : bond 0.00719 ( 8) metal coordination : angle 1.65819 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5403.85 seconds wall clock time: 93 minutes 29.46 seconds (5609.46 seconds total)