Starting phenix.real_space_refine on Fri Aug 7 05:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ppt_17815/08_2026/8ppt_17815.map" } resolution = 2.9 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 34 5.49 5 Mg 3 5.21 5 S 75 5.16 5 C 12460 2.51 5 N 3284 2.21 5 O 3761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19620 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3565 Classifications: {'peptide': 447} Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 415} Chain: "C" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "D" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "E" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1939 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 7, 'TRANS': 238} Chain: "P" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "T" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 9535 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1191, 9528 Classifications: {'peptide': 1191} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1123} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 1191, 9528 Classifications: {'peptide': 1191} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1123} Chain breaks: 1 bond proxies already assigned to first conformer: 9723 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15521 SG CYS B 706 17.290 104.259 62.511 1.00 54.10 S ATOM 15543 SG CYS B 709 17.403 105.381 58.905 1.00100.89 S ATOM 15608 SG CYS B 718 20.610 105.185 60.749 1.00 64.77 S ATOM 15629 SG CYS B 721 18.158 107.910 61.682 1.00 75.38 S ATOM 15712 SG CYS B 731 15.107 79.734 61.311 1.00 85.25 S ATOM 15736 SG CYS B 734 13.188 81.340 58.312 1.00 95.21 S ATOM 15864 SG CYS B 750 11.595 81.073 61.795 1.00 97.06 S ATOM 15886 SG CYS B 753 11.995 77.991 59.934 1.00124.80 S ATOM 18877 SG CYS B1123 49.506 74.372 52.322 1.00 70.79 S ATOM 18899 SG CYS B1126 45.772 75.042 52.835 1.00 76.08 S ATOM 19005 SG CYS B1139 47.292 71.696 51.155 1.00 96.74 S ATOM 19025 SG CYS B1142 46.485 75.243 49.687 1.00107.69 S Time building chain proxies: 6.08, per 1000 atoms: 0.31 Number of scatterers: 19620 At special positions: 0 Unit cell: (116.96, 145.34, 148.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 75 16.00 P 34 15.00 Mg 3 11.99 O 3761 8.00 N 3284 7.00 C 12460 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: 1.50 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 709 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 718 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 721 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 706 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 753 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 731 " pdb="ZN ZN B1302 " - pdb=" SG CYS B 734 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1126 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1142 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1139 " pdb="ZN ZN B1303 " - pdb=" SG CYS B1123 " Number of angles added : 18 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 20 sheets defined 34.5% alpha, 20.4% beta 14 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.623A pdb=" N VAL A 206 " --> pdb=" O VAL A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 removed outlier: 4.084A pdb=" N ILE A 223 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.601A pdb=" N ASN A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 removed outlier: 3.921A pdb=" N LYS A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 415 through 419 removed outlier: 3.651A pdb=" N LEU A 419 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 436 Processing helix chain 'A' and resid 464 through 473 Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.661A pdb=" N VAL A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 527 Processing helix chain 'A' and resid 584 through 590 Processing helix chain 'C' and resid 9 through 22 removed outlier: 3.614A pdb=" N PHE C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 81 Processing helix chain 'C' and resid 138 through 152 removed outlier: 3.784A pdb=" N LEU C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'D' and resid 9 through 22 removed outlier: 3.613A pdb=" N PHE D 13 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 138 through 152 Processing helix chain 'D' and resid 201 through 209 Processing helix chain 'E' and resid 9 through 21 removed outlier: 3.627A pdb=" N PHE E 13 " --> pdb=" O GLY E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 138 through 152 removed outlier: 4.110A pdb=" N LEU E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER E 152 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 209 Processing helix chain 'B' and resid 6 through 30 removed outlier: 3.784A pdb=" N ILE B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 59 through 71 removed outlier: 4.376A pdb=" N ARG B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.513A pdb=" N SER B 150 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 removed outlier: 3.762A pdb=" N GLN B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 removed outlier: 3.570A pdb=" N HIS B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 213 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 272 through 283 Processing helix chain 'B' and resid 311 through 324 Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.781A pdb=" N LYS B 332 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.557A pdb=" N ALA B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.612A pdb=" N PHE B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 486 through 498 Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 517 through 529 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 539 through 543 removed outlier: 3.765A pdb=" N VAL B 543 " --> pdb=" O TRP B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 558 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 607 through 615 removed outlier: 4.053A pdb=" N ALA B 611 " --> pdb=" O TYR B 607 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 613 " --> pdb=" O TRP B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 631 through 640 Processing helix chain 'B' and resid 686 through 693 Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.902A pdb=" N GLY B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 779 removed outlier: 3.783A pdb=" N LEU B 770 " --> pdb=" O ARG B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 812 removed outlier: 3.787A pdb=" N GLY B 805 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 849 Processing helix chain 'B' and resid 876 through 897 removed outlier: 3.650A pdb=" N LYS B 885 " --> pdb=" O ARG B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 913 removed outlier: 3.916A pdb=" N ILE B 913 " --> pdb=" O GLU B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 950 Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 996 through 1000 removed outlier: 3.794A pdb=" N VAL B1000 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1007 removed outlier: 3.597A pdb=" N ASN B1006 " --> pdb=" O GLU B1003 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B1007 " --> pdb=" O VAL B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1022 removed outlier: 3.769A pdb=" N TYR B1018 " --> pdb=" O PRO B1014 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B1022 " --> pdb=" O TYR B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1026 through 1031 removed outlier: 3.580A pdb=" N VAL B1031 " --> pdb=" O LYS B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1040 Processing helix chain 'B' and resid 1066 through 1071 removed outlier: 3.877A pdb=" N LEU B1071 " --> pdb=" O TYR B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1088 Processing helix chain 'B' and resid 1092 through 1117 removed outlier: 4.049A pdb=" N VAL B1096 " --> pdb=" O ASP B1092 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLU B1098 " --> pdb=" O HIS B1094 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS B1104 " --> pdb=" O ILE B1100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B1105 " --> pdb=" O LEU B1101 " (cutoff:3.500A) Proline residue: B1107 - end of helix removed outlier: 4.006A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1155 Processing helix chain 'B' and resid 1158 through 1169 removed outlier: 3.666A pdb=" N TYR B1169 " --> pdb=" O LEU B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1172 through 1190 removed outlier: 4.007A pdb=" N PHE B1190 " --> pdb=" O ILE B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1215 Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 removed outlier: 6.089A pdb=" N VAL A 485 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 556 " --> pdb=" O VAL A 575 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 567 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 565 " --> pdb=" O ASN A 576 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 272 removed outlier: 3.774A pdb=" N VAL A 267 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ALA A 318 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE A 334 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LYS A 320 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 297 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LYS A 333 " --> pdb=" O PHE A 297 " (cutoff:3.500A) removed outlier: 12.119A pdb=" N TYR A 335 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 284 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 477 through 479 removed outlier: 6.312A pdb=" N MET A 444 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TYR A 354 " --> pdb=" O TYR A 398 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ILE A 400 " --> pdb=" O TYR A 354 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 356 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 357 " --> pdb=" O PRO A 600 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 599 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL A 612 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL A 601 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 608 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.774A pdb=" N LYS C 60 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE C 3 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS C 93 " --> pdb=" O PHE C 3 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N THR C 108 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS D 178 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU D 169 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N SER D 154 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.578A pdb=" N VAL C 31 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 71 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA C 27 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU C 26 " --> pdb=" O MET C 41 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N MET C 41 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ALA C 28 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG C 39 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 52 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG C 238 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 239 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 231 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS C 133 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 189 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 135 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 200 removed outlier: 6.538A pdb=" N SER C 154 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLU C 169 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 179 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 174 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 178 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR E 108 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS E 60 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 61 through 62 removed outlier: 4.856A pdb=" N THR D 108 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS E 178 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 174 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU E 169 " --> pdb=" O SER E 154 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER E 154 " --> pdb=" O GLU E 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 67 through 72 removed outlier: 3.763A pdb=" N VAL D 71 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA D 27 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU D 26 " --> pdb=" O MET D 41 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET D 41 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ALA D 28 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG D 39 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR D 232 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLU D 216 " --> pdb=" O TYR D 232 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP D 188 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU D 137 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU D 186 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 67 through 72 removed outlier: 3.673A pdb=" N VAL E 71 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA E 27 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLU E 26 " --> pdb=" O MET E 41 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N MET E 41 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ALA E 28 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ARG E 39 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS E 30 " --> pdb=" O SER E 37 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE E 49 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 239 " --> pdb=" O TYR E 231 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR E 231 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR E 232 " --> pdb=" O GLU E 216 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU E 216 " --> pdb=" O TYR E 232 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP E 188 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU E 137 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU E 186 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 43 through 44 removed outlier: 7.633A pdb=" N GLY B 941 " --> pdb=" O ASP B 824 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR B 826 " --> pdb=" O GLY B 941 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA B 943 " --> pdb=" O THR B 826 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA B 828 " --> pdb=" O ALA B 943 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU B 875 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 935 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 122 through 129 removed outlier: 6.944A pdb=" N TYR B 142 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL B 125 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ALA B 140 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ILE B 127 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR B 138 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 437 through 441 removed outlier: 6.008A pdb=" N ARG B 351 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ILE B 441 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG B 353 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 365 through 367 Processing sheet with id=AB6, first strand: chain 'B' and resid 414 through 416 removed outlier: 6.442A pdb=" N ILE B 406 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.867A pdb=" N GLU B 560 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 575 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLU B 562 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 697 through 701 removed outlier: 3.616A pdb=" N ILE B 701 " --> pdb=" O ALA B 761 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 761 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AC1, first strand: chain 'B' and resid 832 through 833 Processing sheet with id=AC2, first strand: chain 'B' and resid 1129 through 1130 811 hydrogen bonds defined for protein. 2235 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 41 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 3.86 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4647 1.33 - 1.45: 3930 1.45 - 1.58: 11289 1.58 - 1.70: 66 1.70 - 1.82: 132 Bond restraints: 20064 Sorted by residual: bond pdb=" C3' DG P 17 " pdb=" C2' DG P 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.25e+00 bond pdb=" C3' DC T 14 " pdb=" C2' DC T 14 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.66e+00 bond pdb=" C3' DT T 15 " pdb=" C2' DT T 15 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.65e+00 bond pdb=" C3' DC T 24 " pdb=" C2' DC T 24 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.59e+00 bond pdb=" C3' DC P 9 " pdb=" C2' DC P 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.58e+00 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 26091 1.22 - 2.45: 896 2.45 - 3.67: 206 3.67 - 4.89: 43 4.89 - 6.11: 11 Bond angle restraints: 27247 Sorted by residual: angle pdb=" N VAL B1141 " pdb=" CA VAL B1141 " pdb=" C VAL B1141 " ideal model delta sigma weight residual 111.77 107.22 4.55 1.04e+00 9.25e-01 1.92e+01 angle pdb=" N3 DT T 15 " pdb=" C4 DT T 15 " pdb=" O4 DT T 15 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT P 16 " pdb=" C4 DT P 16 " pdb=" O4 DT P 16 " ideal model delta sigma weight residual 119.90 122.32 -2.42 6.00e-01 2.78e+00 1.63e+01 angle pdb=" N PRO A 211 " pdb=" CA PRO A 211 " pdb=" CB PRO A 211 " ideal model delta sigma weight residual 103.15 99.29 3.86 9.70e-01 1.06e+00 1.58e+01 angle pdb=" O4 DT T 15 " pdb=" C4 DT T 15 " pdb=" C5 DT T 15 " ideal model delta sigma weight residual 124.90 122.12 2.78 7.00e-01 2.04e+00 1.58e+01 ... (remaining 27242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 11545 35.73 - 71.46: 605 71.46 - 107.20: 29 107.20 - 142.93: 0 142.93 - 178.66: 2 Dihedral angle restraints: 12181 sinusoidal: 5288 harmonic: 6893 Sorted by residual: dihedral pdb=" CA LYS B 668 " pdb=" C LYS B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLU B1093 " pdb=" C GLU B1093 " pdb=" N HIS B1094 " pdb=" CA HIS B1094 " ideal model delta harmonic sigma weight residual 180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TYR B1047 " pdb=" C TYR B1047 " pdb=" N TYR B1048 " pdb=" CA TYR B1048 " ideal model delta harmonic sigma weight residual 180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 12178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2463 0.054 - 0.107: 500 0.107 - 0.161: 89 0.161 - 0.215: 0 0.215 - 0.268: 1 Chirality restraints: 3053 Sorted by residual: chirality pdb=" CB VAL B1141 " pdb=" CA VAL B1141 " pdb=" CG1 VAL B1141 " pdb=" CG2 VAL B1141 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" C3' DG P 5 " pdb=" C4' DG P 5 " pdb=" O3' DG P 5 " pdb=" C2' DG P 5 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 3050 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 208 " -0.015 2.00e-02 2.50e+03 3.11e-02 9.67e+00 pdb=" C LEU A 208 " 0.054 2.00e-02 2.50e+03 pdb=" O LEU A 208 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 209 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 235 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" CG ASP C 235 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP C 235 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 235 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO B 146 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.030 5.00e-02 4.00e+02 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 100 2.54 - 3.13: 13606 3.13 - 3.72: 28254 3.72 - 4.31: 40354 4.31 - 4.90: 70334 Nonbonded interactions: 152648 Sorted by model distance: nonbonded pdb=" OD1 ASN A 450 " pdb="MG MG A 701 " model vdw 1.950 2.170 nonbonded pdb=" OD2 ASP A 404 " pdb="MG MG A 701 " model vdw 2.124 2.170 nonbonded pdb=" ND1 HIS A 560 " pdb="MG MG A 701 " model vdw 2.166 2.250 nonbonded pdb=" O SER B 149 " pdb=" OG SER B 149 " model vdw 2.182 3.040 nonbonded pdb=" O THR A 595 " pdb=" OG1 THR A 595 " model vdw 2.196 3.040 ... (remaining 152643 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 'C' selection = chain 'D' selection = chain 'E' } 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=0.46 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: 5.610 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.480 Find NCS groups from input model: 0.110 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.003 0.035 20076 Z= 0.201 Angle : 0.597 21.614 27265 Z= 0.335 Chirality : 0.045 0.268 3053 Planarity : 0.004 0.054 3393 Dihedral : 19.224 178.659 7745 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.82 % Allowed : 30.71 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.19 (0.17), residues: 2366 helix: 1.04 (0.20), residues: 700 sheet: 0.24 (0.23), residues: 523 loop : -1.04 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 92 TYR 0.016 0.001 TYR B 138 PHE 0.011 0.001 PHE A 463 TRP 0.009 0.001 TRP B 552 HIS 0.003 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.20 (20064) covalent geometry : angle 0.56812 / 0.33 (27247) hydrogen bonds : bond 0.19791 / 13.06 ( 852) hydrogen bonds : angle 6.88070 / 4.67 ( 2317) metal coordination : bond 0.00795 / 0.40 ( 12) metal coordination : angle 7.18062 / 3.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 351 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6747 (pt0) REVERT: C 190 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6938 (mt-10) REVERT: D 127 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7471 (mp0) REVERT: B 667 MET cc_start: 0.8716 (mtt) cc_final: 0.8210 (mtt) outliers start: 58 outliers final: 55 residues processed: 274 average time/residue: 0.5423 time to fit residues: 168.9338 Evaluate side-chains 265 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 210 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 476 ASN Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 149 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 768 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1026 SER Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1149 THR Chi-restraints excluded: chain B residue 1181 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.3980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN B1198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.194042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.142372 restraints weight = 34730.918| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.35 r_work: 0.3524 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20076 Z= 0.128 Angle : 0.586 21.068 27265 Z= 0.302 Chirality : 0.045 0.244 3053 Planarity : 0.004 0.049 3393 Dihedral : 13.043 179.903 3005 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.94 % Allowed : 28.62 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.01 (0.17), residues: 2366 helix: 1.20 (0.19), residues: 717 sheet: 0.22 (0.22), residues: 554 loop : -0.89 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 92 TYR 0.013 0.001 TYR D 231 PHE 0.012 0.001 PHE B 443 TRP 0.009 0.001 TRP B 552 HIS 0.003 0.001 HIS B 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (20064) covalent geometry : angle 0.55894 / 0.30 (27247) hydrogen bonds : bond 0.05144 / 3.40 ( 852) hydrogen bonds : angle 5.53114 / 3.74 ( 2317) metal coordination : bond 0.00733 / 0.39 ( 12) metal coordination : angle 6.90713 / 3.18 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 224 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7572 (mptt) REVERT: A 351 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6775 (pt0) REVERT: C 147 ASP cc_start: 0.7749 (m-30) cc_final: 0.7528 (m-30) REVERT: C 181 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6971 (mm) REVERT: D 127 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7536 (mp0) REVERT: E 62 GLU cc_start: 0.6855 (pp20) cc_final: 0.6602 (mp0) REVERT: E 227 MET cc_start: 0.7780 (ptm) cc_final: 0.7546 (ptm) REVERT: B 254 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7314 (mp) REVERT: B 792 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7303 (mtp) REVERT: B 1212 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7122 (mp) outliers start: 81 outliers final: 30 residues processed: 282 average time/residue: 0.6231 time to fit residues: 198.4336 Evaluate side-chains 254 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 31 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 HIS E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.193260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.154419 restraints weight = 28995.562| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.32 r_work: 0.3385 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20076 Z= 0.152 Angle : 0.606 21.130 27265 Z= 0.305 Chirality : 0.046 0.259 3053 Planarity : 0.005 0.051 3393 Dihedral : 12.892 179.292 2953 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.66 % Allowed : 28.23 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.07 (0.17), residues: 2366 helix: 1.17 (0.19), residues: 718 sheet: 0.13 (0.22), residues: 556 loop : -0.93 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 92 TYR 0.015 0.001 TYR B1047 PHE 0.014 0.001 PHE A 463 TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (20064) covalent geometry : angle 0.57781 / 0.30 (27247) hydrogen bonds : bond 0.04749 / 3.12 ( 852) hydrogen bonds : angle 5.15333 / 3.48 ( 2317) metal coordination : bond 0.00844 / 0.44 ( 12) metal coordination : angle 7.15284 / 3.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 222 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7592 (mptt) REVERT: C 147 ASP cc_start: 0.7686 (m-30) cc_final: 0.7414 (m-30) REVERT: C 165 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7723 (m) REVERT: C 181 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6901 (mm) REVERT: C 184 GLU cc_start: 0.7772 (tp30) cc_final: 0.7410 (tm-30) REVERT: C 190 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7199 (mt-10) REVERT: D 127 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7496 (mp0) REVERT: D 143 GLU cc_start: 0.7391 (mp0) cc_final: 0.7014 (mp0) REVERT: D 225 MET cc_start: 0.7576 (ptt) cc_final: 0.6540 (pp-130) REVERT: B 254 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7280 (mp) REVERT: B 321 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7065 (ttmt) REVERT: B 625 MET cc_start: 0.8124 (mmp) cc_final: 0.7459 (mtp) REVERT: B 663 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8278 (tttm) REVERT: B 1212 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6951 (mp) outliers start: 96 outliers final: 45 residues processed: 290 average time/residue: 0.6153 time to fit residues: 201.8734 Evaluate side-chains 272 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 178 optimal weight: 0.2980 chunk 232 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.192857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139215 restraints weight = 32253.847| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.63 r_work: 0.3458 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20076 Z= 0.156 Angle : 0.604 20.855 27265 Z= 0.305 Chirality : 0.046 0.259 3053 Planarity : 0.005 0.052 3393 Dihedral : 12.738 179.452 2947 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.86 % Allowed : 27.79 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.11 (0.17), residues: 2366 helix: 1.12 (0.19), residues: 718 sheet: 0.13 (0.22), residues: 554 loop : -0.97 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 92 TYR 0.015 0.001 TYR D 231 PHE 0.014 0.001 PHE A 463 TRP 0.008 0.001 TRP B 622 HIS 0.004 0.001 HIS B 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (20064) covalent geometry : angle 0.57587 / 0.30 (27247) hydrogen bonds : bond 0.04589 / 3.01 ( 852) hydrogen bonds : angle 5.01801 / 3.39 ( 2317) metal coordination : bond 0.00830 / 0.43 ( 12) metal coordination : angle 7.08025 / 3.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 221 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7613 (mptt) REVERT: A 351 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6349 (mt-10) REVERT: C 147 ASP cc_start: 0.7657 (m-30) cc_final: 0.7402 (m-30) REVERT: C 181 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6879 (mm) REVERT: C 190 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: D 73 MET cc_start: 0.7895 (mmp) cc_final: 0.7637 (mmp) REVERT: D 127 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7508 (mp0) REVERT: D 143 GLU cc_start: 0.7449 (mp0) cc_final: 0.7116 (mp0) REVERT: D 225 MET cc_start: 0.7582 (ptt) cc_final: 0.6605 (pp-130) REVERT: E 233 ILE cc_start: 0.6372 (mm) cc_final: 0.5718 (pt) REVERT: B 254 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7131 (mp) REVERT: B 353 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8687 (mtt180) REVERT: B 625 MET cc_start: 0.7929 (mmp) cc_final: 0.7331 (mtp) REVERT: B 663 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8223 (tttm) REVERT: B 1212 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7095 (mp) outliers start: 100 outliers final: 51 residues processed: 296 average time/residue: 0.6361 time to fit residues: 212.7366 Evaluate side-chains 272 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 444 MET Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 619 CYS Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 78 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.192434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139384 restraints weight = 36197.215| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.55 r_work: 0.3473 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20076 Z= 0.183 Angle : 0.636 21.317 27265 Z= 0.318 Chirality : 0.047 0.260 3053 Planarity : 0.005 0.052 3393 Dihedral : 12.693 179.427 2939 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.10 % Allowed : 28.04 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.22 (0.17), residues: 2366 helix: 1.01 (0.19), residues: 717 sheet: 0.09 (0.22), residues: 557 loop : -1.03 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 39 TYR 0.017 0.002 TYR B1047 PHE 0.015 0.002 PHE B 467 TRP 0.009 0.001 TRP B 622 HIS 0.005 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.18 (20064) covalent geometry : angle 0.60727 / 0.32 (27247) hydrogen bonds : bond 0.04882 / 3.20 ( 852) hydrogen bonds : angle 4.98412 / 3.37 ( 2317) metal coordination : bond 0.00912 / 0.47 ( 12) metal coordination : angle 7.37155 / 3.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 223 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7584 (mptt) REVERT: A 306 ARG cc_start: 0.7589 (ppt90) cc_final: 0.7169 (tpm170) REVERT: A 351 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6418 (mt-10) REVERT: C 41 MET cc_start: 0.8928 (ttp) cc_final: 0.8663 (ttp) REVERT: C 181 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6761 (mm) REVERT: C 190 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7423 (mt-10) REVERT: D 73 MET cc_start: 0.8014 (mmp) cc_final: 0.7766 (mmp) REVERT: D 74 ASP cc_start: 0.8137 (t0) cc_final: 0.7861 (t0) REVERT: D 127 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: D 133 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.7071 (ttpp) REVERT: D 143 GLU cc_start: 0.7531 (mp0) cc_final: 0.7225 (mp0) REVERT: D 169 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7074 (tp30) REVERT: D 225 MET cc_start: 0.7603 (ptt) cc_final: 0.6602 (pp-130) REVERT: D 236 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: E 82 ARG cc_start: 0.8393 (mmm160) cc_final: 0.8144 (mmm160) REVERT: E 233 ILE cc_start: 0.6423 (mm) cc_final: 0.5759 (pt) REVERT: B 254 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7259 (mp) REVERT: B 353 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8775 (mtt180) REVERT: B 578 SER cc_start: 0.7554 (m) cc_final: 0.7071 (p) REVERT: B 625 MET cc_start: 0.8274 (mmp) cc_final: 0.7606 (mtp) REVERT: B 663 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8365 (tttm) REVERT: B 1212 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7126 (mp) outliers start: 105 outliers final: 65 residues processed: 302 average time/residue: 0.6284 time to fit residues: 214.0711 Evaluate side-chains 294 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 219 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 475 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 701 ILE Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 52 optimal weight: 9.9990 chunk 208 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 162 optimal weight: 0.5980 chunk 215 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 227 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 230 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN E 162 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.197243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.158034 restraints weight = 31731.251| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 4.24 r_work: 0.3439 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20076 Z= 0.116 Angle : 0.565 20.034 27265 Z= 0.286 Chirality : 0.044 0.257 3053 Planarity : 0.004 0.052 3393 Dihedral : 12.581 179.424 2939 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.03 % Allowed : 29.40 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.00 (0.17), residues: 2366 helix: 1.24 (0.20), residues: 712 sheet: 0.20 (0.22), residues: 551 loop : -0.90 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 39 TYR 0.015 0.001 TYR B 138 PHE 0.011 0.001 PHE B 443 TRP 0.007 0.001 TRP A 379 HIS 0.003 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (20064) covalent geometry : angle 0.53784 / 0.28 (27247) hydrogen bonds : bond 0.03905 / 2.57 ( 852) hydrogen bonds : angle 4.76882 / 3.22 ( 2317) metal coordination : bond 0.00725 / 0.39 ( 12) metal coordination : angle 6.74595 / 3.11 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 226 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7581 (mptt) REVERT: A 306 ARG cc_start: 0.7626 (ppt90) cc_final: 0.7132 (tpm170) REVERT: A 351 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6314 (mt-10) REVERT: C 41 MET cc_start: 0.8952 (ttp) cc_final: 0.8702 (ttp) REVERT: C 181 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6600 (mm) REVERT: C 190 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: C 235 ASP cc_start: 0.8358 (m-30) cc_final: 0.7980 (t0) REVERT: D 73 MET cc_start: 0.7992 (mmp) cc_final: 0.7765 (mmp) REVERT: D 74 ASP cc_start: 0.8044 (t0) cc_final: 0.7743 (t0) REVERT: D 127 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7533 (mp0) REVERT: D 133 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7043 (ttpp) REVERT: D 143 GLU cc_start: 0.7428 (mp0) cc_final: 0.7179 (mp0) REVERT: D 155 MET cc_start: 0.8304 (ttt) cc_final: 0.8090 (ttm) REVERT: D 169 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7026 (tp30) REVERT: D 225 MET cc_start: 0.7611 (ptt) cc_final: 0.6632 (pp-130) REVERT: D 236 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: E 82 ARG cc_start: 0.8380 (mmm160) cc_final: 0.8169 (mmm160) REVERT: E 155 MET cc_start: 0.8206 (ttm) cc_final: 0.7948 (ttp) REVERT: E 162 ASN cc_start: 0.8064 (OUTLIER) cc_final: 0.7332 (t0) REVERT: E 233 ILE cc_start: 0.6415 (mm) cc_final: 0.5752 (pt) REVERT: B 254 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7102 (mp) REVERT: B 353 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8774 (mtt180) REVERT: B 625 MET cc_start: 0.8189 (mmp) cc_final: 0.7554 (mtp) REVERT: B 663 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8290 (tttm) REVERT: B 1187 ASP cc_start: 0.7902 (m-30) cc_final: 0.7699 (t0) REVERT: B 1212 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7106 (mp) outliers start: 83 outliers final: 43 residues processed: 290 average time/residue: 0.6240 time to fit residues: 204.3979 Evaluate side-chains 271 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1196 GLU Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 43 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 183 optimal weight: 0.0270 chunk 199 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN E 162 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 ASN B1198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.197288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158672 restraints weight = 30706.514| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 3.83 r_work: 0.3411 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20076 Z= 0.118 Angle : 0.568 20.100 27265 Z= 0.286 Chirality : 0.044 0.257 3053 Planarity : 0.004 0.049 3393 Dihedral : 12.511 179.466 2937 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.13 % Allowed : 29.35 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.05 (0.17), residues: 2366 helix: 1.31 (0.20), residues: 711 sheet: 0.22 (0.22), residues: 546 loop : -0.89 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 92 TYR 0.014 0.001 TYR B 138 PHE 0.011 0.001 PHE B 443 TRP 0.008 0.001 TRP A 379 HIS 0.002 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (20064) covalent geometry : angle 0.54174 / 0.28 (27247) hydrogen bonds : bond 0.03865 / 2.55 ( 852) hydrogen bonds : angle 4.70681 / 3.18 ( 2317) metal coordination : bond 0.00744 / 0.40 ( 12) metal coordination : angle 6.67765 / 3.08 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 225 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7602 (mptt) REVERT: A 306 ARG cc_start: 0.7639 (ppt90) cc_final: 0.7129 (tpm170) REVERT: C 41 MET cc_start: 0.8965 (ttp) cc_final: 0.8706 (ttp) REVERT: C 181 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6518 (mm) REVERT: C 190 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: C 235 ASP cc_start: 0.8367 (m-30) cc_final: 0.7987 (t0) REVERT: D 73 MET cc_start: 0.8019 (mmp) cc_final: 0.7715 (mmp) REVERT: D 74 ASP cc_start: 0.8078 (t0) cc_final: 0.7773 (t0) REVERT: D 127 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7548 (mp0) REVERT: D 133 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7260 (tmmm) REVERT: D 143 GLU cc_start: 0.7552 (mp0) cc_final: 0.7274 (mp0) REVERT: D 169 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7089 (tp30) REVERT: D 225 MET cc_start: 0.7561 (ptt) cc_final: 0.6645 (pp-130) REVERT: D 236 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: E 155 MET cc_start: 0.8246 (ttm) cc_final: 0.8028 (ttp) REVERT: E 162 ASN cc_start: 0.7842 (OUTLIER) cc_final: 0.7069 (t0) REVERT: E 176 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7693 (tt0) REVERT: E 233 ILE cc_start: 0.6486 (mm) cc_final: 0.5825 (pt) REVERT: B 254 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7131 (mp) REVERT: B 353 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8738 (mtt180) REVERT: B 480 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8654 (pt0) REVERT: B 625 MET cc_start: 0.8271 (mmp) cc_final: 0.7631 (mtp) REVERT: B 663 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8338 (tttm) REVERT: B 1187 ASP cc_start: 0.7932 (m-30) cc_final: 0.7714 (t0) REVERT: B 1212 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7088 (mp) outliers start: 85 outliers final: 50 residues processed: 294 average time/residue: 0.6586 time to fit residues: 218.4051 Evaluate side-chains 281 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 219 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 104 GLN Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 169 GLU Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1057 ASP Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 99 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 4 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.188349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147178 restraints weight = 21409.708| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.77 r_work: 0.3433 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.127 20076 Z= 0.399 Angle : 0.839 23.016 27265 Z= 0.418 Chirality : 0.057 0.292 3053 Planarity : 0.006 0.054 3393 Dihedral : 12.876 179.804 2937 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.71 % Allowed : 28.91 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: -0.64 (0.17), residues: 2366 helix: 0.53 (0.19), residues: 717 sheet: -0.07 (0.22), residues: 551 loop : -1.23 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 994 TYR 0.025 0.003 TYR B1047 PHE 0.023 0.003 PHE A 425 TRP 0.012 0.003 TRP B 622 HIS 0.010 0.002 HIS B1104 Details of bonding type rmsd/Z covalent geometry : bond 0.01030 / 0.40 (20064) covalent geometry : angle 0.81064 / 0.42 (27247) hydrogen bonds : bond 0.06558 / 4.29 ( 852) hydrogen bonds : angle 5.18017 / 3.51 ( 2317) metal coordination : bond 0.01217 / 0.64 ( 12) metal coordination : angle 8.39549 / 3.93 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 217 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7627 (mptt) REVERT: A 351 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6385 (mt-10) REVERT: C 41 MET cc_start: 0.9075 (ttp) cc_final: 0.8794 (ttm) REVERT: C 190 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7521 (mt-10) REVERT: C 235 ASP cc_start: 0.8445 (m-30) cc_final: 0.8022 (t0) REVERT: D 73 MET cc_start: 0.8154 (mmp) cc_final: 0.7919 (mmp) REVERT: D 127 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: D 143 GLU cc_start: 0.7557 (mp0) cc_final: 0.7265 (mp0) REVERT: D 155 MET cc_start: 0.8441 (ttt) cc_final: 0.8160 (ttm) REVERT: D 169 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7333 (tp30) REVERT: E 22 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7479 (ttp-170) REVERT: E 233 ILE cc_start: 0.6412 (mm) cc_final: 0.5727 (pt) REVERT: B 254 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7419 (mp) REVERT: B 353 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8776 (mtt180) REVERT: B 506 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8007 (mt-10) REVERT: B 656 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8243 (ttt) REVERT: B 663 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8431 (tttm) REVERT: B 769 GLU cc_start: 0.7785 (mp0) cc_final: 0.7462 (mp0) REVERT: B 812 ASP cc_start: 0.8633 (t0) cc_final: 0.8350 (t0) outliers start: 97 outliers final: 64 residues processed: 293 average time/residue: 0.6678 time to fit residues: 221.6307 Evaluate side-chains 286 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 214 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 176 GLU Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1045 GLU Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1098 GLU Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1196 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 136 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.195578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.156633 restraints weight = 35002.789| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 4.92 r_work: 0.3377 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20076 Z= 0.130 Angle : 0.611 21.043 27265 Z= 0.309 Chirality : 0.046 0.258 3053 Planarity : 0.005 0.050 3393 Dihedral : 12.708 179.405 2937 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.26 % Allowed : 30.42 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.30 (0.17), residues: 2366 helix: 0.95 (0.19), residues: 717 sheet: 0.03 (0.22), residues: 558 loop : -1.07 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 92 TYR 0.017 0.001 TYR B 138 PHE 0.012 0.001 PHE A 463 TRP 0.009 0.001 TRP B 622 HIS 0.003 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (20064) covalent geometry : angle 0.58299 / 0.31 (27247) hydrogen bonds : bond 0.04263 / 2.79 ( 852) hydrogen bonds : angle 4.83957 / 3.27 ( 2317) metal coordination : bond 0.00761 / 0.41 ( 12) metal coordination : angle 7.17332 / 3.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 217 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7576 (mptt) REVERT: A 351 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6366 (mt-10) REVERT: C 41 MET cc_start: 0.9014 (ttp) cc_final: 0.8757 (ttm) REVERT: C 190 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: C 235 ASP cc_start: 0.8360 (m-30) cc_final: 0.7988 (t0) REVERT: D 73 MET cc_start: 0.8037 (mmp) cc_final: 0.7751 (mmp) REVERT: D 74 ASP cc_start: 0.8043 (t0) cc_final: 0.7754 (t0) REVERT: D 127 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: D 143 GLU cc_start: 0.7496 (mp0) cc_final: 0.7277 (mp0) REVERT: D 155 MET cc_start: 0.8371 (ttt) cc_final: 0.8048 (ttm) REVERT: D 169 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7236 (tp30) REVERT: E 155 MET cc_start: 0.8220 (ttm) cc_final: 0.7993 (ttp) REVERT: E 233 ILE cc_start: 0.6388 (mm) cc_final: 0.5717 (pt) REVERT: B 254 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7119 (mp) REVERT: B 353 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8786 (mtt180) REVERT: B 578 SER cc_start: 0.7639 (m) cc_final: 0.7101 (p) REVERT: B 625 MET cc_start: 0.8297 (mmp) cc_final: 0.7607 (mtp) REVERT: B 663 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8362 (tttm) REVERT: B 1212 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6959 (mp) outliers start: 67 outliers final: 50 residues processed: 270 average time/residue: 0.6412 time to fit residues: 195.3317 Evaluate side-chains 268 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 238 ARG Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 353 ARG Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 chunk 175 optimal weight: 0.0000 chunk 114 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN E 75 HIS ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1198 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.193657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139991 restraints weight = 32498.902| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.40 r_work: 0.3496 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20076 Z= 0.140 Angle : 0.606 21.192 27265 Z= 0.304 Chirality : 0.045 0.256 3053 Planarity : 0.005 0.051 3393 Dihedral : 12.620 179.288 2937 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.16 % Allowed : 30.61 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.21 (0.17), residues: 2366 helix: 1.06 (0.19), residues: 717 sheet: 0.06 (0.22), residues: 557 loop : -1.03 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 92 TYR 0.016 0.001 TYR B 138 PHE 0.012 0.001 PHE A 463 TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (20064) covalent geometry : angle 0.57847 / 0.30 (27247) hydrogen bonds : bond 0.04210 / 2.76 ( 852) hydrogen bonds : angle 4.74799 / 3.21 ( 2317) metal coordination : bond 0.00830 / 0.44 ( 12) metal coordination : angle 7.10448 / 3.28 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7623 (mptt) REVERT: A 351 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6333 (mt-10) REVERT: C 41 MET cc_start: 0.9013 (ttp) cc_final: 0.8771 (ttm) REVERT: C 190 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7369 (mt-10) REVERT: C 235 ASP cc_start: 0.8317 (m-30) cc_final: 0.7953 (t0) REVERT: D 73 MET cc_start: 0.8023 (mmp) cc_final: 0.7736 (mmp) REVERT: D 74 ASP cc_start: 0.8090 (t0) cc_final: 0.7810 (t0) REVERT: D 127 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: D 155 MET cc_start: 0.8393 (ttt) cc_final: 0.8085 (ttm) REVERT: D 169 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7197 (tp30) REVERT: D 236 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: E 155 MET cc_start: 0.8201 (ttm) cc_final: 0.7959 (ttp) REVERT: E 233 ILE cc_start: 0.6508 (mm) cc_final: 0.5850 (pt) REVERT: B 254 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7174 (mp) REVERT: B 578 SER cc_start: 0.7562 (m) cc_final: 0.7084 (p) REVERT: B 625 MET cc_start: 0.8245 (mmp) cc_final: 0.7599 (mtp) REVERT: B 652 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 663 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8354 (tttm) REVERT: B 1212 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7067 (mp) outliers start: 65 outliers final: 48 residues processed: 269 average time/residue: 0.6030 time to fit residues: 183.4023 Evaluate side-chains 272 residues out of total 2056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 216 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 663 LYS Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 826 THR Chi-restraints excluded: chain B residue 962 VAL Chi-restraints excluded: chain B residue 992 THR Chi-restraints excluded: chain B residue 1001 ASP Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1047 TYR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1108 ASP Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 VAL Chi-restraints excluded: chain B residue 1161 THR Chi-restraints excluded: chain B residue 1181 LEU Chi-restraints excluded: chain B residue 1212 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 161 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 193 optimal weight: 0.0970 chunk 106 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 52 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.197398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159736 restraints weight = 34997.818| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 4.86 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3873 r_free = 0.3873 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (18 function evaluations) r_final: 0.3873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20076 Z= 0.118 Angle : 0.583 20.233 27265 Z= 0.294 Chirality : 0.045 0.256 3053 Planarity : 0.004 0.049 3393 Dihedral : 12.543 179.407 2937 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.87 % Allowed : 31.15 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.09 (0.17), residues: 2366 helix: 1.19 (0.20), residues: 712 sheet: 0.15 (0.22), residues: 546 loop : -0.98 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 92 TYR 0.016 0.001 TYR A 197 PHE 0.011 0.001 PHE B 443 TRP 0.008 0.001 TRP A 379 HIS 0.002 0.001 HIS B 944 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (20064) covalent geometry : angle 0.55708 / 0.29 (27247) hydrogen bonds : bond 0.03808 / 2.50 ( 852) hydrogen bonds : angle 4.64845 / 3.14 ( 2317) metal coordination : bond 0.00719 / 0.38 ( 12) metal coordination : angle 6.70103 / 3.09 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7325.29 seconds wall clock time: 125 minutes 11.06 seconds (7511.06 seconds total)