Starting phenix.real_space_refine on Wed Mar 4 15:51:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yes_33776/03_2026/7yes_33776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yes_33776/03_2026/7yes_33776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yes_33776/03_2026/7yes_33776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yes_33776/03_2026/7yes_33776.map" model { file = "/net/cci-nas-00/data/ceres_data/7yes_33776/03_2026/7yes_33776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yes_33776/03_2026/7yes_33776.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 77 5.16 5 C 9369 2.51 5 N 2480 2.21 5 O 2752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 14679 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1369, 10906 Classifications: {'peptide': 1369} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 69, 'TRANS': 1297} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "B" Number of atoms: 2011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 260, 1983 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1990 Chain: "C" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 733 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 515 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 513 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 65} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9165 SG CYS A1150 49.054 41.877 96.212 1.00 68.18 S ATOM 9187 SG CYS A1153 52.215 39.556 95.959 1.00 71.87 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN B 244 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 244 " occ=0.50 residue: pdb=" N ASER B 266 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 266 " occ=0.50 residue: pdb=" N ACYS B 275 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 275 " occ=0.50 residue: pdb=" N ATHR B 335 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 335 " occ=0.50 Time building chain proxies: 3.52, per 1000 atoms: 0.24 Number of scatterers: 14679 At special positions: 0 Unit cell: (178.45, 134.46, 111.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 77 16.00 O 2752 8.00 N 2480 7.00 C 9369 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: 1.65 Conformation dependent library (CDL) restraints added in 961.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A1345 " pdb="ZN ZN A2301 " - pdb=" NE2 HIS A1347 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1150 " pdb="ZN ZN A2301 " - pdb=" SG CYS A1153 " Number of angles added : 2 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3566 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 7 sheets defined 56.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.543A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 4.060A pdb=" N CYS A 44 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.782A pdb=" N LYS A 54 " --> pdb=" O TYR A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 63 Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.565A pdb=" N LYS A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 113 through 122 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 145 through 166 removed outlier: 3.756A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.748A pdb=" N MET A 210 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP A 211 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.963A pdb=" N GLU A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 221' Processing helix chain 'A' and resid 235 through 261 removed outlier: 3.641A pdb=" N GLU A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.633A pdb=" N ILE A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 381 through 391 removed outlier: 3.864A pdb=" N ILE A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.535A pdb=" N SER A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 436 removed outlier: 3.509A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 450 through 454 removed outlier: 3.595A pdb=" N MET A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 464 removed outlier: 3.584A pdb=" N LEU A 464 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.927A pdb=" N ILE A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.505A pdb=" N LEU A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 567 through 584 removed outlier: 3.944A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 609 Processing helix chain 'A' and resid 633 through 640 removed outlier: 3.868A pdb=" N LEU A 638 " --> pdb=" O LYS A 635 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 640 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 656 Proline residue: A 647 - end of helix removed outlier: 3.630A pdb=" N TYR A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 669 removed outlier: 3.544A pdb=" N TYR A 667 " --> pdb=" O ASN A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 731 Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.887A pdb=" N GLN A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 820 removed outlier: 3.533A pdb=" N THR A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 850 removed outlier: 3.715A pdb=" N GLU A 850 " --> pdb=" O ARG A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 875 removed outlier: 3.679A pdb=" N ARG A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 866 " --> pdb=" O ALA A 862 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 867 " --> pdb=" O PHE A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 903 removed outlier: 3.688A pdb=" N ILE A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 905 No H-bonds generated for 'chain 'A' and resid 904 through 905' Processing helix chain 'A' and resid 906 through 910 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 929 through 943 removed outlier: 3.581A pdb=" N ILE A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 954 removed outlier: 3.721A pdb=" N ILE A 953 " --> pdb=" O PHE A 949 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 954 " --> pdb=" O LEU A 950 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 949 through 954' Processing helix chain 'A' and resid 963 through 968 removed outlier: 3.599A pdb=" N LEU A 967 " --> pdb=" O ILE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 995 removed outlier: 3.531A pdb=" N LEU A 984 " --> pdb=" O LEU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1005 Processing helix chain 'A' and resid 1008 through 1021 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.558A pdb=" N ALA A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1048 Processing helix chain 'A' and resid 1054 through 1059 Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 3.710A pdb=" N ASN A1065 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A1066 " --> pdb=" O ASN A1063 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1062 through 1066' Processing helix chain 'A' and resid 1069 through 1085 removed outlier: 3.633A pdb=" N ARG A1073 " --> pdb=" O PRO A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1100 Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1134 through 1138 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1213 through 1230 removed outlier: 3.943A pdb=" N ARG A1217 " --> pdb=" O SER A1213 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A1230 " --> pdb=" O LEU A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1245 removed outlier: 3.907A pdb=" N LYS A1241 " --> pdb=" O ASP A1237 " (cutoff:3.500A) Proline residue: A1242 - end of helix Processing helix chain 'A' and resid 1267 through 1273 Processing helix chain 'A' and resid 1287 through 1290 removed outlier: 3.550A pdb=" N THR A1290 " --> pdb=" O ASN A1287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1287 through 1290' Processing helix chain 'A' and resid 1296 through 1300 Processing helix chain 'A' and resid 1315 through 1331 removed outlier: 3.828A pdb=" N ILE A1320 " --> pdb=" O PHE A1316 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN A1321 " --> pdb=" O GLN A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1339 removed outlier: 3.513A pdb=" N ILE A1339 " --> pdb=" O ALA A1336 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1374 removed outlier: 4.240A pdb=" N ARG A1373 " --> pdb=" O ASP A1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 118 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 127 through 149 removed outlier: 3.690A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'B' and resid 177 through 187 removed outlier: 4.037A pdb=" N GLU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 237 through 254 removed outlier: 3.750A pdb=" N GLN B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 285 through 288 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'C' and resid 82 through 118 removed outlier: 3.812A pdb=" N LEU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 143 removed outlier: 3.893A pdb=" N SER C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.776A pdb=" N GLU C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 112 Processing helix chain 'D' and resid 113 through 146 removed outlier: 3.989A pdb=" N GLY D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Proline residue: D 120 - end of helix removed outlier: 3.907A pdb=" N SER D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 144 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 144 removed outlier: 4.649A pdb=" N LYS E 119 " --> pdb=" O GLU E 115 " (cutoff:3.500A) Proline residue: E 120 - end of helix removed outlier: 3.844A pdb=" N LEU E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA3, first strand: chain 'A' and resid 549 through 552 Processing sheet with id=AA4, first strand: chain 'A' and resid 734 through 740 removed outlier: 3.873A pdb=" N LYS A 734 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 630 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 793 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 801 Processing sheet with id=AA6, first strand: chain 'A' and resid 1139 through 1141 Processing sheet with id=AA7, first strand: chain 'B' and resid 294 through 296 removed outlier: 6.342A pdb=" N ILE B 295 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N CYS B 326 " --> pdb=" O LEU B 338 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2041 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: 2.54 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4764 1.34 - 1.46: 2398 1.46 - 1.57: 7740 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 15014 Sorted by residual: bond pdb=" N ILE A1267 " pdb=" CA ILE A1267 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ASN A1266 " pdb=" CA ASN A1266 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.06e+00 bond pdb=" N GLY A1265 " pdb=" CA GLY A1265 " ideal model delta sigma weight residual 1.449 1.478 -0.029 1.14e-02 7.69e+03 6.32e+00 bond pdb=" N GLN A 608 " pdb=" CA GLN A 608 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.30e-02 5.92e+03 6.22e+00 bond pdb=" N GLN A 814 " pdb=" CA GLN A 814 " ideal model delta sigma weight residual 1.465 1.488 -0.023 1.31e-02 5.83e+03 2.95e+00 ... (remaining 15009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 20043 1.67 - 3.33: 316 3.33 - 5.00: 45 5.00 - 6.67: 15 6.67 - 8.33: 5 Bond angle restraints: 20424 Sorted by residual: angle pdb=" C THR A 756 " pdb=" N ASP A 757 " pdb=" CA ASP A 757 " ideal model delta sigma weight residual 121.54 129.29 -7.75 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C PHE A 526 " pdb=" N SER A 527 " pdb=" CA SER A 527 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" CA GLY A1265 " pdb=" C GLY A1265 " pdb=" O GLY A1265 " ideal model delta sigma weight residual 121.11 117.75 3.36 9.00e-01 1.23e+00 1.39e+01 angle pdb=" C ALA A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 121.54 128.58 -7.04 1.91e+00 2.74e-01 1.36e+01 angle pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 ... (remaining 20419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 8123 17.67 - 35.34: 760 35.34 - 53.01: 137 53.01 - 70.68: 21 70.68 - 88.35: 13 Dihedral angle restraints: 9054 sinusoidal: 3555 harmonic: 5499 Sorted by residual: dihedral pdb=" CA ILE A1191 " pdb=" C ILE A1191 " pdb=" N PRO A1192 " pdb=" CA PRO A1192 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASP A 110 " pdb=" C ASP A 110 " pdb=" N ALA A 111 " pdb=" CA ALA A 111 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA LEU A 112 " pdb=" C LEU A 112 " pdb=" N PHE A 113 " pdb=" CA PHE A 113 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 9051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1556 0.033 - 0.066: 564 0.066 - 0.098: 158 0.098 - 0.131: 57 0.131 - 0.164: 9 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CA PRO A1192 " pdb=" N PRO A1192 " pdb=" C PRO A1192 " pdb=" CB PRO A1192 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CB ILE A1267 " pdb=" CA ILE A1267 " pdb=" CG1 ILE A1267 " pdb=" CG2 ILE A1267 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CG LEU A 114 " pdb=" CB LEU A 114 " pdb=" CD1 LEU A 114 " pdb=" CD2 LEU A 114 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 2341 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1191 " -0.069 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO A1192 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A1192 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A1192 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 303 " -0.034 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 304 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 467 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 468 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " 0.028 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1551 2.75 - 3.29: 14332 3.29 - 3.82: 23440 3.82 - 4.36: 26472 4.36 - 4.90: 48195 Nonbonded interactions: 113990 Sorted by model distance: nonbonded pdb=" O TYR A 32 " pdb=" OG1 THR A 70 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP A 10 " pdb=" OG SER A 14 " model vdw 2.248 3.040 nonbonded pdb=" NH1 ARG B 298 " pdb=" OG SER B 299 " model vdw 2.253 3.120 nonbonded pdb=" O GLU A 643 " pdb=" OG1 THR B 148 " model vdw 2.261 3.040 nonbonded pdb=" O TYR A 667 " pdb=" NE2 GLN A 671 " model vdw 2.275 3.120 ... (remaining 113985 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 'D' and (resid 82 through 118 or (resid 119 and (name N or name CA or nam \ e C or name O or name CB )) or resid 120 through 146)) selection = (chain 'E' and (resid 82 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 146)) } 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=0.50 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.930 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.002 0.040 15018 Z= 0.120 Angle : 0.532 8.333 20426 Z= 0.281 Chirality : 0.039 0.164 2344 Planarity : 0.004 0.105 2618 Dihedral : 14.108 88.352 5488 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.75 % Favored : 92.60 % Rotamer: Outliers : 0.18 % Allowed : 0.31 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.21), residues: 1863 helix: 2.15 (0.18), residues: 976 sheet: 1.30 (0.56), residues: 89 loop : -1.55 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 133 TYR 0.010 0.001 TYR A 800 PHE 0.013 0.001 PHE A1011 TRP 0.025 0.001 TRP A1085 HIS 0.004 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00242 (15014) covalent geometry : angle 0.53172 (20424) hydrogen bonds : bond 0.14346 ( 719) hydrogen bonds : angle 4.26340 ( 2041) metal coordination : bond 0.00466 ( 4) metal coordination : angle 2.31485 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.559 Fit side-chains REVERT: A 594 MET cc_start: 0.6406 (tpp) cc_final: 0.6057 (tpt) REVERT: A 602 LYS cc_start: 0.8559 (tppp) cc_final: 0.8046 (ttpt) REVERT: A 1013 ASP cc_start: 0.7210 (m-30) cc_final: 0.6853 (m-30) REVERT: A 1054 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8765 (ttm-80) outliers start: 2 outliers final: 0 residues processed: 209 average time/residue: 0.1501 time to fit residues: 43.7974 Evaluate side-chains 172 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 307 GLN A 446 ASN A 608 GLN E 132 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.104587 restraints weight = 58740.526| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 5.68 r_work: 0.2722 rms_B_bonded: 5.66 restraints_weight: 2.0000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15018 Z= 0.125 Angle : 0.550 11.165 20426 Z= 0.284 Chirality : 0.040 0.162 2344 Planarity : 0.005 0.106 2618 Dihedral : 3.978 27.648 2014 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.70 % Favored : 92.71 % Rotamer: Outliers : 0.92 % Allowed : 6.54 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.21), residues: 1863 helix: 2.11 (0.17), residues: 992 sheet: 1.33 (0.56), residues: 89 loop : -1.45 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 133 TYR 0.021 0.001 TYR A1088 PHE 0.015 0.001 PHE A1011 TRP 0.013 0.001 TRP A 191 HIS 0.006 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00282 (15014) covalent geometry : angle 0.54975 (20424) hydrogen bonds : bond 0.04152 ( 719) hydrogen bonds : angle 3.61376 ( 2041) metal coordination : bond 0.00464 ( 4) metal coordination : angle 2.60581 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.579 Fit side-chains REVERT: A 678 ASP cc_start: 0.8120 (t0) cc_final: 0.7796 (m-30) REVERT: B 329 GLN cc_start: 0.7337 (tm-30) cc_final: 0.7088 (tm-30) outliers start: 14 outliers final: 12 residues processed: 184 average time/residue: 0.1525 time to fit residues: 39.4441 Evaluate side-chains 182 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 143 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 85 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 43 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: A 120 ASN A 324 HIS A 352 HIS A 446 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.134580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.101126 restraints weight = 39899.256| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 5.44 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 15018 Z= 0.233 Angle : 0.649 10.511 20426 Z= 0.335 Chirality : 0.044 0.158 2344 Planarity : 0.005 0.109 2618 Dihedral : 4.530 27.613 2014 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.67 % Favored : 91.57 % Rotamer: Outliers : 1.85 % Allowed : 9.37 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1863 helix: 1.89 (0.17), residues: 993 sheet: 1.14 (0.56), residues: 89 loop : -1.59 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 923 TYR 0.024 0.002 TYR A 427 PHE 0.021 0.002 PHE A 411 TRP 0.020 0.002 TRP A 191 HIS 0.008 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00585 (15014) covalent geometry : angle 0.64686 (20424) hydrogen bonds : bond 0.05597 ( 719) hydrogen bonds : angle 3.73027 ( 2041) metal coordination : bond 0.00896 ( 4) metal coordination : angle 4.71881 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 608 GLN cc_start: 0.7937 (pt0) cc_final: 0.7477 (mm110) REVERT: A 1015 MET cc_start: 0.7869 (mtp) cc_final: 0.7467 (mtp) REVERT: A 1380 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7143 (mm) outliers start: 28 outliers final: 21 residues processed: 182 average time/residue: 0.1516 time to fit residues: 38.8111 Evaluate side-chains 183 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 122 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 558 ASN B 213 ASN E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.101187 restraints weight = 54809.268| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 5.31 r_work: 0.2693 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15018 Z= 0.123 Angle : 0.547 10.839 20426 Z= 0.283 Chirality : 0.040 0.161 2344 Planarity : 0.004 0.107 2618 Dihedral : 4.258 27.862 2014 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.21 % Favored : 93.08 % Rotamer: Outliers : 1.36 % Allowed : 11.34 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1863 helix: 1.96 (0.17), residues: 1003 sheet: 1.17 (0.56), residues: 89 loop : -1.56 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.011 0.001 TYR A 427 PHE 0.021 0.001 PHE A1011 TRP 0.013 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00284 (15014) covalent geometry : angle 0.54599 (20424) hydrogen bonds : bond 0.03872 ( 719) hydrogen bonds : angle 3.50793 ( 2041) metal coordination : bond 0.00471 ( 4) metal coordination : angle 2.69443 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.567 Fit side-chains REVERT: A 235 ASP cc_start: 0.8762 (m-30) cc_final: 0.8516 (m-30) REVERT: A 453 MET cc_start: 0.8144 (ppp) cc_final: 0.7648 (tpt) REVERT: A 608 GLN cc_start: 0.7918 (pt0) cc_final: 0.7289 (mm110) outliers start: 20 outliers final: 18 residues processed: 178 average time/residue: 0.1519 time to fit residues: 38.1045 Evaluate side-chains 176 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 137 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 115 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 54 optimal weight: 0.0010 chunk 159 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 328 ASN B 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.136280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.100632 restraints weight = 59575.924| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 5.48 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15018 Z= 0.150 Angle : 0.559 11.171 20426 Z= 0.288 Chirality : 0.041 0.162 2344 Planarity : 0.005 0.106 2618 Dihedral : 4.249 27.796 2014 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.24 % Favored : 92.06 % Rotamer: Outliers : 2.10 % Allowed : 11.78 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1863 helix: 2.03 (0.17), residues: 994 sheet: 1.17 (0.56), residues: 89 loop : -1.59 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 133 TYR 0.012 0.001 TYR A 427 PHE 0.016 0.002 PHE A 411 TRP 0.013 0.001 TRP A 191 HIS 0.006 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00364 (15014) covalent geometry : angle 0.55817 (20424) hydrogen bonds : bond 0.04164 ( 719) hydrogen bonds : angle 3.47393 ( 2041) metal coordination : bond 0.00613 ( 4) metal coordination : angle 3.42874 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.552 Fit side-chains REVERT: A 235 ASP cc_start: 0.8277 (m-30) cc_final: 0.8041 (m-30) REVERT: A 386 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 608 GLN cc_start: 0.7991 (pt0) cc_final: 0.7483 (mm110) REVERT: A 1011 PHE cc_start: 0.8444 (t80) cc_final: 0.8204 (t80) REVERT: A 1015 MET cc_start: 0.8080 (mtp) cc_final: 0.7755 (mtp) REVERT: A 1380 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7154 (mm) outliers start: 32 outliers final: 25 residues processed: 187 average time/residue: 0.1507 time to fit residues: 40.4067 Evaluate side-chains 188 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 77 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A1149 GLN B 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104144 restraints weight = 48769.783| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 5.77 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 15018 Z= 0.178 Angle : 0.582 11.244 20426 Z= 0.300 Chirality : 0.042 0.178 2344 Planarity : 0.005 0.107 2618 Dihedral : 4.331 27.913 2014 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.13 % Favored : 92.17 % Rotamer: Outliers : 2.03 % Allowed : 12.45 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1863 helix: 1.97 (0.17), residues: 994 sheet: 1.14 (0.56), residues: 89 loop : -1.60 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.012 0.001 TYR A 701 PHE 0.017 0.002 PHE A 411 TRP 0.014 0.001 TRP A 191 HIS 0.007 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00443 (15014) covalent geometry : angle 0.58111 (20424) hydrogen bonds : bond 0.04443 ( 719) hydrogen bonds : angle 3.50420 ( 2041) metal coordination : bond 0.00596 ( 4) metal coordination : angle 3.75588 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.572 Fit side-chains REVERT: A 235 ASP cc_start: 0.8231 (m-30) cc_final: 0.7985 (m-30) REVERT: A 386 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8317 (tt) REVERT: A 608 GLN cc_start: 0.8020 (pt0) cc_final: 0.7623 (mm110) REVERT: A 1015 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7791 (mtp) REVERT: A 1313 ASN cc_start: 0.7912 (t0) cc_final: 0.7238 (t0) REVERT: A 1380 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7143 (mm) outliers start: 31 outliers final: 24 residues processed: 180 average time/residue: 0.1394 time to fit residues: 35.7596 Evaluate side-chains 183 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 135 CYS Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 144 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 143 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 115 optimal weight: 8.9990 chunk 68 optimal weight: 0.0050 chunk 136 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 62 optimal weight: 0.0670 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1149 GLN B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.139294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.108065 restraints weight = 51219.512| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 6.09 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15018 Z= 0.100 Angle : 0.523 11.191 20426 Z= 0.269 Chirality : 0.039 0.162 2344 Planarity : 0.004 0.105 2618 Dihedral : 4.050 28.662 2014 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.10 % Favored : 93.19 % Rotamer: Outliers : 1.36 % Allowed : 13.56 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1863 helix: 2.10 (0.17), residues: 1004 sheet: 1.19 (0.56), residues: 89 loop : -1.52 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.009 0.001 TYR A1049 PHE 0.021 0.001 PHE A1011 TRP 0.012 0.001 TRP A1085 HIS 0.004 0.000 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00212 (15014) covalent geometry : angle 0.52213 (20424) hydrogen bonds : bond 0.03125 ( 719) hydrogen bonds : angle 3.33715 ( 2041) metal coordination : bond 0.00531 ( 4) metal coordination : angle 2.49083 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.429 Fit side-chains REVERT: A 166 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7300 (ptt-90) REVERT: A 608 GLN cc_start: 0.7925 (pt0) cc_final: 0.7614 (mm110) REVERT: A 1313 ASN cc_start: 0.7759 (t0) cc_final: 0.6894 (t0) REVERT: A 1380 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7076 (mm) outliers start: 20 outliers final: 13 residues processed: 179 average time/residue: 0.1369 time to fit residues: 34.3674 Evaluate side-chains 178 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 142 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 144 optimal weight: 0.4980 chunk 97 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 159 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 171 optimal weight: 30.0000 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN A1149 GLN B 213 ASN E 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102877 restraints weight = 61627.596| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 5.70 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15018 Z= 0.112 Angle : 0.534 10.994 20426 Z= 0.274 Chirality : 0.039 0.163 2344 Planarity : 0.004 0.105 2618 Dihedral : 4.022 28.597 2014 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.37 % Favored : 92.92 % Rotamer: Outliers : 1.36 % Allowed : 13.81 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1863 helix: 2.11 (0.17), residues: 1007 sheet: 1.27 (0.57), residues: 89 loop : -1.50 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 133 TYR 0.010 0.001 TYR B 176 PHE 0.021 0.001 PHE A 793 TRP 0.011 0.001 TRP A 191 HIS 0.006 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00256 (15014) covalent geometry : angle 0.53285 (20424) hydrogen bonds : bond 0.03373 ( 719) hydrogen bonds : angle 3.31785 ( 2041) metal coordination : bond 0.00428 ( 4) metal coordination : angle 2.81803 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.478 Fit side-chains REVERT: A 166 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7274 (ptt-90) REVERT: A 608 GLN cc_start: 0.8008 (pt0) cc_final: 0.7576 (mm110) REVERT: A 1313 ASN cc_start: 0.7799 (t0) cc_final: 0.6920 (t0) REVERT: A 1380 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7145 (mm) outliers start: 20 outliers final: 16 residues processed: 174 average time/residue: 0.1452 time to fit residues: 35.8936 Evaluate side-chains 182 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 168 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN A1149 GLN B 213 ASN E 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102136 restraints weight = 60487.005| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 5.62 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15018 Z= 0.125 Angle : 0.544 10.887 20426 Z= 0.280 Chirality : 0.040 0.175 2344 Planarity : 0.004 0.105 2618 Dihedral : 4.086 28.694 2014 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.02 % Favored : 92.33 % Rotamer: Outliers : 1.60 % Allowed : 13.63 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.21), residues: 1863 helix: 2.11 (0.17), residues: 1002 sheet: 1.27 (0.57), residues: 89 loop : -1.53 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 133 TYR 0.010 0.001 TYR A 117 PHE 0.036 0.001 PHE A1011 TRP 0.012 0.001 TRP A 191 HIS 0.006 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00298 (15014) covalent geometry : angle 0.54301 (20424) hydrogen bonds : bond 0.03609 ( 719) hydrogen bonds : angle 3.35264 ( 2041) metal coordination : bond 0.00441 ( 4) metal coordination : angle 3.13609 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.464 Fit side-chains REVERT: A 166 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7304 (ptt-90) REVERT: A 386 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8401 (tt) REVERT: A 608 GLN cc_start: 0.8047 (pt0) cc_final: 0.7581 (mm110) REVERT: A 1313 ASN cc_start: 0.7832 (t0) cc_final: 0.7012 (t0) REVERT: A 1380 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7172 (mm) outliers start: 24 outliers final: 19 residues processed: 175 average time/residue: 0.1332 time to fit residues: 33.3489 Evaluate side-chains 184 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 87 optimal weight: 0.0020 chunk 98 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1149 GLN B 213 ASN E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.104027 restraints weight = 74141.881| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 6.34 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15018 Z= 0.107 Angle : 0.534 10.968 20426 Z= 0.275 Chirality : 0.039 0.171 2344 Planarity : 0.004 0.105 2618 Dihedral : 4.006 28.793 2014 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.65 % Favored : 92.71 % Rotamer: Outliers : 1.48 % Allowed : 14.00 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1863 helix: 2.14 (0.17), residues: 1006 sheet: 1.29 (0.57), residues: 89 loop : -1.52 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 133 TYR 0.009 0.001 TYR B 176 PHE 0.026 0.001 PHE A1011 TRP 0.011 0.001 TRP A 191 HIS 0.005 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00242 (15014) covalent geometry : angle 0.53303 (20424) hydrogen bonds : bond 0.03267 ( 719) hydrogen bonds : angle 3.31003 ( 2041) metal coordination : bond 0.00530 ( 4) metal coordination : angle 2.73169 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3726 Ramachandran restraints generated. 1863 Oldfield, 0 Emsley, 1863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.624 Fit side-chains REVERT: A 166 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7287 (ptt-90) REVERT: A 386 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8330 (tt) REVERT: A 608 GLN cc_start: 0.8024 (pt0) cc_final: 0.7551 (mm110) REVERT: A 1015 MET cc_start: 0.8096 (mtp) cc_final: 0.7772 (mtp) REVERT: A 1313 ASN cc_start: 0.7817 (t0) cc_final: 0.6924 (t0) REVERT: A 1380 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7127 (mm) outliers start: 22 outliers final: 17 residues processed: 175 average time/residue: 0.1448 time to fit residues: 36.0491 Evaluate side-chains 183 residues out of total 1645 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 803 LYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1044 LEU Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1149 GLN B 213 ASN E 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.106365 restraints weight = 49967.950| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 6.07 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15018 Z= 0.128 Angle : 0.548 10.817 20426 Z= 0.281 Chirality : 0.040 0.174 2344 Planarity : 0.004 0.105 2618 Dihedral : 4.069 29.008 2014 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.19 % Favored : 92.17 % Rotamer: Outliers : 1.79 % Allowed : 13.69 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.21), residues: 1863 helix: 2.08 (0.17), residues: 1011 sheet: 1.24 (0.59), residues: 84 loop : -1.51 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 133 TYR 0.011 0.001 TYR A 117 PHE 0.035 0.001 PHE A1011 TRP 0.011 0.001 TRP A 191 HIS 0.006 0.001 HIS C 166 Details of bonding type rmsd covalent geometry : bond 0.00305 (15014) covalent geometry : angle 0.54689 (20424) hydrogen bonds : bond 0.03645 ( 719) hydrogen bonds : angle 3.33251 ( 2041) metal coordination : bond 0.00469 ( 4) metal coordination : angle 3.27708 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.65 seconds wall clock time: 55 minutes 19.41 seconds (3319.41 seconds total)