Starting phenix.real_space_refine on Fri Mar 6 18:11:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ufg_26475/03_2026/7ufg_26475.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ufg_26475/03_2026/7ufg_26475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ufg_26475/03_2026/7ufg_26475.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ufg_26475/03_2026/7ufg_26475.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ufg_26475/03_2026/7ufg_26475.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ufg_26475/03_2026/7ufg_26475.map" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 129 5.16 5 C 11503 2.51 5 N 3129 2.21 5 O 3482 1.98 5 H 14783 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33028 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 15782 Classifications: {'peptide': 1151} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 4, 'PTRANS': 64, 'TRANS': 1082} Chain breaks: 3 Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 9, 'GLU:plan': 15, 'HIS:plan': 2, 'GLN:plan1': 10, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 16506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 16506 Classifications: {'peptide': 1182} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 4, 'PTRANS': 67, 'TRANS': 1110} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 403 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "C" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 335 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.99, per 1000 atoms: 0.18 Number of scatterers: 33028 At special positions: 0 Unit cell: (105.41, 123.67, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 129 16.00 O 3482 8.00 N 3129 7.00 C 11503 6.00 H 14783 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 507 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 577 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 532 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 801 " distance=2.03 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 755 " distance=2.03 Simple disulfide: pdb=" SG CYS A 695 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 867 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 891 " distance=2.03 Simple disulfide: pdb=" SG CYS A 903 " - pdb=" SG CYS A 910 " distance=2.03 Simple disulfide: pdb=" SG CYS A 919 " - pdb=" SG CYS A 931 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A 990 " distance=2.03 Simple disulfide: pdb=" SG CYS A 971 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1125 " distance=2.03 Simple disulfide: pdb=" SG CYS A1130 " - pdb=" SG CYS B1130 " distance=2.03 Simple disulfide: pdb=" SG CYS A1135 " - pdb=" SG CYS A1189 " distance=2.03 Simple disulfide: pdb=" SG CYS A1147 " - pdb=" SG CYS A1158 " distance=2.03 Simple disulfide: pdb=" SG CYS A1162 " - pdb=" SG CYS A1200 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1249 " distance=2.03 Simple disulfide: pdb=" SG CYS A1220 " - pdb=" SG CYS A1230 " distance=2.03 Simple disulfide: pdb=" SG CYS A1234 " - pdb=" SG CYS A1262 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS B 507 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 577 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 532 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 673 " - pdb=" SG CYS B 755 " distance=2.03 Simple disulfide: pdb=" SG CYS B 695 " - pdb=" SG CYS B 701 " distance=2.03 Simple disulfide: pdb=" SG CYS B 867 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 880 " - pdb=" SG CYS B 891 " distance=2.03 Simple disulfide: pdb=" SG CYS B 903 " - pdb=" SG CYS B 910 " distance=2.03 Simple disulfide: pdb=" SG CYS B 919 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B 956 " - pdb=" SG CYS B 990 " distance=2.03 Simple disulfide: pdb=" SG CYS B 971 " - pdb=" SG CYS B1059 " distance=2.03 Simple disulfide: pdb=" SG CYS B1112 " - pdb=" SG CYS B1125 " distance=2.03 Simple disulfide: pdb=" SG CYS B1135 " - pdb=" SG CYS B1189 " distance=2.03 Simple disulfide: pdb=" SG CYS B1147 " - pdb=" SG CYS B1158 " distance=2.03 Simple disulfide: pdb=" SG CYS B1162 " - pdb=" SG CYS B1200 " distance=2.03 Simple disulfide: pdb=" SG CYS B1205 " - pdb=" SG CYS B1249 " distance=2.03 Simple disulfide: pdb=" SG CYS B1220 " - pdb=" SG CYS B1230 " distance=2.03 Simple disulfide: pdb=" SG CYS B1234 " - pdb=" SG CYS B1262 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A4000 " pdb="ZN ZN A4000 " - pdb=" NE2 HIS A 492 " pdb="ZN ZN A4000 " - pdb=" NE2 HIS A 486 " pdb="ZN ZN A4000 " - pdb=" NE2 HIS A 482 " pdb=" ZN B4000 " pdb="ZN ZN B4000 " - pdb=" NE2 HIS B 492 " pdb="ZN ZN B4000 " - pdb=" NE2 HIS B 482 " pdb="ZN ZN B4000 " - pdb=" NE2 HIS B 486 " 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 37 sheets defined 15.0% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.958A pdb=" N ALA A 303 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 304 " --> pdb=" O HIS A 300 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.715A pdb=" N MET A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 482 " --> pdb=" O HIS A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 removed outlier: 3.512A pdb=" N GLU A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 628 through 632 removed outlier: 4.174A pdb=" N HIS A 631 " --> pdb=" O SER A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 981 through 985 removed outlier: 3.507A pdb=" N GLN A 984 " --> pdb=" O GLY A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 removed outlier: 3.936A pdb=" N ALA A1000 " --> pdb=" O SER A 997 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A1001 " --> pdb=" O GLN A 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 997 through 1001' Processing helix chain 'A' and resid 1105 through 1110 Processing helix chain 'B' and resid 149 through 154 removed outlier: 4.489A pdb=" N LYS B 154 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 212 through 216 removed outlier: 4.334A pdb=" N ALA B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 212 through 216' Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 265 through 269 removed outlier: 3.634A pdb=" N ARG B 268 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 269 " --> pdb=" O SER B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 265 through 269' Processing helix chain 'B' and resid 291 through 306 Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 335 through 340 removed outlier: 4.162A pdb=" N GLY B 340 " --> pdb=" O SER B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 426 removed outlier: 3.634A pdb=" N LEU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 488 removed outlier: 4.243A pdb=" N MET B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 568 through 582 Processing helix chain 'B' and resid 583 through 586 Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.626A pdb=" N GLU B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 920 through 924 Processing helix chain 'B' and resid 927 through 932 Processing helix chain 'B' and resid 958 through 962 removed outlier: 4.148A pdb=" N ILE B 961 " --> pdb=" O GLY B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 981 through 985 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.745A pdb=" N LEU B 999 " --> pdb=" O PRO B 995 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B1000 " --> pdb=" O TYR B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1112 removed outlier: 3.698A pdb=" N LEU B1109 " --> pdb=" O ASP B1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 140 removed outlier: 3.766A pdb=" N VAL D 132 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'C' and resid 126 through 139 removed outlier: 3.890A pdb=" N GLU C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 132 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 137 " --> pdb=" O LYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 140 removed outlier: 6.830A pdb=" N LEU A 130 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 139 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 115 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 47 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP A 44 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS A 175 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG A 46 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE A 173 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 140 removed outlier: 6.830A pdb=" N LEU A 130 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 139 " --> pdb=" O MET A 128 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET A 128 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 115 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 47 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP A 44 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N HIS A 175 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ARG A 46 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE A 173 " --> pdb=" O ARG A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 93 removed outlier: 6.763A pdb=" N ILE A 77 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL A 56 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 59 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 159 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 321 removed outlier: 3.694A pdb=" N GLU A 314 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL A 320 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N LEU A 433 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ARG A 274 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE A 435 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ARG A 276 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N PHE A 437 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N VAL A 278 " --> pdb=" O PHE A 437 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 434 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LEU A 466 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 436 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AA6, first strand: chain 'A' and resid 600 through 603 removed outlier: 7.048A pdb=" N THR A 610 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 640 through 642 Processing sheet with id=AA8, first strand: chain 'A' and resid 645 through 647 removed outlier: 6.283A pdb=" N TYR A 771 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 772 " --> pdb=" O LEU A 739 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 746 " --> pdb=" O LEU A 738 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 805 through 811 removed outlier: 3.829A pdb=" N SER A 847 " --> pdb=" O GLU A 850 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU A 850 " --> pdb=" O SER A 847 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 805 through 811 Processing sheet with id=AB2, first strand: chain 'A' and resid 891 through 892 removed outlier: 3.767A pdb=" N ARG A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 901 through 902 Processing sheet with id=AB4, first strand: chain 'A' and resid 939 through 943 removed outlier: 7.770A pdb=" N ILE A1093 " --> pdb=" O VAL A1024 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1024 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A1095 " --> pdb=" O HIS A1022 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 946 through 949 removed outlier: 6.617A pdb=" N LEU A1043 " --> pdb=" O GLN A1080 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A1082 " --> pdb=" O GLN A1041 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN A1041 " --> pdb=" O VAL A1082 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A1084 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER A1039 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE A1086 " --> pdb=" O THR A1037 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N THR A1037 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY A1053 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A1042 " --> pdb=" O ASP A1051 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASP A1051 " --> pdb=" O LEU A1042 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ASP A1044 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER A1049 " --> pdb=" O ASP A1044 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1117 through 1118 Processing sheet with id=AB7, first strand: chain 'A' and resid 1143 through 1147 Processing sheet with id=AB8, first strand: chain 'A' and resid 1175 through 1176 Processing sheet with id=AB9, first strand: chain 'A' and resid 1189 through 1190 Processing sheet with id=AC1, first strand: chain 'A' and resid 1216 through 1218 Processing sheet with id=AC2, first strand: chain 'A' and resid 1239 through 1241 Processing sheet with id=AC3, first strand: chain 'B' and resid 135 through 140 removed outlier: 5.351A pdb=" N GLN B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 132 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP B 44 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N HIS B 175 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG B 46 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE B 173 " --> pdb=" O ARG B 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 135 through 140 removed outlier: 5.351A pdb=" N GLN B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 132 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP B 44 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N HIS B 175 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG B 46 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE B 173 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N HIS B 175 " --> pdb=" O ARG B 15 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N ARG B 15 " --> pdb=" O HIS B 175 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.701A pdb=" N ILE B 77 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL B 56 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 271 through 272 removed outlier: 6.310A pdb=" N LYS B 271 " --> pdb=" O SER B 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 318 through 320 removed outlier: 7.427A pdb=" N LEU B 318 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 277 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 320 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN B 279 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG B 276 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N PHE B 437 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N VAL B 278 " --> pdb=" O PHE B 437 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 600 through 604 removed outlier: 7.012A pdb=" N THR B 610 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 642 removed outlier: 6.693A pdb=" N GLU B 783 " --> pdb=" O THR B 721 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP B 719 " --> pdb=" O ASP B 785 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA B 787 " --> pdb=" O THR B 717 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR B 717 " --> pdb=" O ALA B 787 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 789 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER B 715 " --> pdb=" O LEU B 789 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER B 791 " --> pdb=" O PRO B 713 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 645 through 647 removed outlier: 6.285A pdb=" N TYR B 771 " --> pdb=" O PHE B 707 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 772 " --> pdb=" O LEU B 739 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP B 735 " --> pdb=" O TYR B 776 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 805 through 811 Processing sheet with id=AD3, first strand: chain 'B' and resid 805 through 811 Processing sheet with id=AD4, first strand: chain 'B' and resid 901 through 904 Processing sheet with id=AD5, first strand: chain 'B' and resid 939 through 943 removed outlier: 7.486A pdb=" N ILE B1093 " --> pdb=" O VAL B1024 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B1024 " --> pdb=" O ILE B1093 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B1095 " --> pdb=" O HIS B1022 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 946 through 949 removed outlier: 6.900A pdb=" N LEU B1043 " --> pdb=" O GLN B1080 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B1082 " --> pdb=" O GLN B1041 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLN B1041 " --> pdb=" O VAL B1082 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B1084 " --> pdb=" O SER B1039 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER B1039 " --> pdb=" O VAL B1084 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE B1086 " --> pdb=" O THR B1037 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N THR B1037 " --> pdb=" O PHE B1086 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE B1038 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B1054 " --> pdb=" O ILE B1038 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL B1040 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1143 through 1147 Processing sheet with id=AD8, first strand: chain 'B' and resid 1166 through 1171 Processing sheet with id=AD9, first strand: chain 'B' and resid 1216 through 1219 Processing sheet with id=AE1, first strand: chain 'B' and resid 1239 through 1241 removed outlier: 3.512A pdb=" N LEU B1261 " --> pdb=" O LYS B1241 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.96 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14779 1.03 - 1.23: 124 1.23 - 1.43: 7974 1.43 - 1.62: 10477 1.62 - 1.82: 159 Bond restraints: 33513 Sorted by residual: bond pdb=" CB VAL A 829 " pdb=" CG1 VAL A 829 " ideal model delta sigma weight residual 1.521 1.573 -0.052 3.30e-02 9.18e+02 2.45e+00 bond pdb=" N HIS A 285 " pdb=" CA HIS A 285 " ideal model delta sigma weight residual 1.458 1.481 -0.023 1.77e-02 3.19e+03 1.69e+00 bond pdb=" CB VAL A 829 " pdb=" CG2 VAL A 829 " ideal model delta sigma weight residual 1.521 1.558 -0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB VAL A 960 " pdb=" CG2 VAL A 960 " ideal model delta sigma weight residual 1.521 1.556 -0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CB ASP A 869 " pdb=" CG ASP A 869 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.04e+00 ... (remaining 33508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.92: 58657 10.92 - 21.85: 43 21.85 - 32.77: 156 32.77 - 43.70: 210 43.70 - 54.62: 59 Bond angle restraints: 59125 Sorted by residual: angle pdb=" C VAL A 975 " pdb=" N ILE A 976 " pdb=" H ILE A 976 " ideal model delta sigma weight residual 124.87 70.25 54.62 3.00e+00 1.11e-01 3.31e+02 angle pdb=" CA ILE A 976 " pdb=" N ILE A 976 " pdb=" H ILE A 976 " ideal model delta sigma weight residual 114.57 60.11 54.46 3.00e+00 1.11e-01 3.30e+02 angle pdb=" C GLU A 282 " pdb=" N ASP A 283 " pdb=" H ASP A 283 " ideal model delta sigma weight residual 124.96 70.79 54.17 3.00e+00 1.11e-01 3.26e+02 angle pdb=" C ILE A 982 " pdb=" N SER A 983 " pdb=" H SER A 983 " ideal model delta sigma weight residual 124.96 70.92 54.04 3.00e+00 1.11e-01 3.24e+02 angle pdb=" CA ASP A 283 " pdb=" N ASP A 283 " pdb=" H ASP A 283 " ideal model delta sigma weight residual 114.66 60.65 54.01 3.00e+00 1.11e-01 3.24e+02 ... (remaining 59120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14800 17.82 - 35.64: 1213 35.64 - 53.45: 346 53.45 - 71.27: 60 71.27 - 89.09: 18 Dihedral angle restraints: 16437 sinusoidal: 8384 harmonic: 8053 Sorted by residual: dihedral pdb=" CB CYS A1112 " pdb=" SG CYS A1112 " pdb=" SG CYS A1125 " pdb=" CB CYS A1125 " ideal model delta sinusoidal sigma weight residual 93.00 27.61 65.39 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CB CYS B 503 " pdb=" SG CYS B 503 " pdb=" SG CYS B 542 " pdb=" CB CYS B 542 " ideal model delta sinusoidal sigma weight residual 93.00 38.66 54.34 1 1.00e+01 1.00e-02 4.00e+01 dihedral pdb=" CB CYS A1130 " pdb=" SG CYS A1130 " pdb=" SG CYS B1130 " pdb=" CB CYS B1130 " ideal model delta sinusoidal sigma weight residual -86.00 -135.78 49.78 1 1.00e+01 1.00e-02 3.40e+01 ... (remaining 16434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 2746 0.347 - 0.693: 41 0.693 - 1.040: 0 1.040 - 1.386: 2 1.386 - 1.733: 26 Chirality restraints: 2815 Sorted by residual: chirality pdb=" CG LEU B 763 " pdb=" CB LEU B 763 " pdb=" CD1 LEU B 763 " pdb=" CD2 LEU B 763 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CG LEU A 242 " pdb=" CB LEU A 242 " pdb=" CD1 LEU A 242 " pdb=" CD2 LEU A 242 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.48e+01 chirality pdb=" CG LEU A 205 " pdb=" CB LEU A 205 " pdb=" CD1 LEU A 205 " pdb=" CD2 LEU A 205 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.34e+01 ... (remaining 2812 not shown) Planarity restraints: 5224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 536 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO A 537 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 537 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 537 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 284 " -0.015 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" N HIS A 285 " 0.014 2.00e-02 2.50e+03 pdb=" CA HIS A 285 " -0.014 2.00e-02 2.50e+03 pdb=" H HIS A 285 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 615 " -0.018 5.00e-02 4.00e+02 2.76e-02 1.22e+00 pdb=" N PRO A 616 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 616 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 616 " -0.015 5.00e-02 4.00e+02 ... (remaining 5221 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 330 1.83 - 2.52: 24740 2.52 - 3.22: 92522 3.22 - 3.91: 121496 3.91 - 4.60: 191107 Nonbonded interactions: 430195 Sorted by model distance: nonbonded pdb=" H HIS A 285 " pdb=" HA HIS A 285 " model vdw 1.140 1.816 nonbonded pdb="HE21 GLN B 42 " pdb=" HH TYR B 118 " model vdw 1.220 2.100 nonbonded pdb=" H VAL A 320 " pdb=" HA VAL A 320 " model vdw 1.412 1.816 nonbonded pdb=" H ARG A1007 " pdb=" HA ARG A1007 " model vdw 1.415 1.816 nonbonded pdb=" H HIS A1055 " pdb=" HA HIS A1055 " model vdw 1.419 1.816 ... (remaining 430190 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1 or name H or name HA \ )) or resid 68 through 80 or (resid 81 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 82 and (name N or name CA or name C or name \ O or name CB or name CG or name OD1 or name OD2)) or (resid 83 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 84 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name OD2)) or resid 85 thr \ ough 326 or (resid 327 and (name N or name CA or name C or name O or name CB or \ name H or name HA or name HB2 or name HB3)) or resid 328 through 333 or (resid 3 \ 34 and (name N or name CA or name C or name O or name CB or name SG )) or resid \ 422 through 442 or (resid 443 and (name N or name CA or name C or name O or name \ CB or name H or name HA or name HB2 or name HB3)) or resid 444 through 589 or ( \ resid 590 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA or name HB2 or name HB3)) or resid 591 through 725 or (resid 726 and (name \ N or name CA or name C or name O or name CB )) or resid 727 or (resid 728 and (n \ ame N or name CA or name C or name O or name CB or name CG or name OD1 or name O \ D2)) or (resid 729 through 730 and (name N or name CA or name C or name O or nam \ e CB or name OG )) or resid 731 through 764 or (resid 765 and (name N or name CA \ or name C or name O or name CB )) or resid 766 through 810 or (resid 811 and (n \ ame N or name CA or name C or name O or name CB or name CG or name OD1 or name O \ D2)) or (resid 812 and (name N or name CA or name C or name O or name CB or name \ CG or name CD )) or resid 813 through 939 or (resid 940 and (name N or name CA \ or name C or name O or name CB or name H or name HA or name HB2 or name HB3)) or \ resid 941 through 959 or (resid 960 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2)) or resid 961 through 993 or (resid 994 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 995 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or (resid 996 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 997 and (na \ me N or name CA or name C or name O or name CB or name OG )) or (resid 998 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name O \ E1 or name NE2)) or (resid 999 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD1 or name CD2)) or (resid 1000 through 1001 and (name \ N or name CA or name C or name O or name CB )) or resid 1002 through 1073 or (re \ sid 1074 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name NE2)) or (resid 1075 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD )) or resid 1076 through 1131 or (resi \ d 1132 and (name N or name CA or name C or name O or name CB )) or resid 1133 th \ rough 1141 or (resid 1142 through 1143 and (name N or name CA or name C or name \ O or name CB )) or resid 1144 through 1162 or (resid 1163 and (name N or name CA \ or name C or name O or name CB )) or resid 1164 through 1170 or (resid 1171 thr \ ough 1172 and (name N or name CA or name C or name O or name CB )) or resid 1184 \ or (resid 1185 through 1186 and (name N or name CA or name C or name O or name \ CB )) or resid 1187 through 1190 or (resid 1191 and (name N or name CA or name C \ or name O or name CB )) or resid 1192 through 1195 or (resid 1196 and (name N o \ r name CA or name C or name O or name CB or name CG )) or resid 1197 through 120 \ 0 or (resid 1201 and (name N or name CA or name C or name O or name CB )) or res \ id 1202 through 1203 or (resid 1204 and (name N or name CA or name C or name O o \ r name CB )) or resid 1205 through 1221 or (resid 1222 and (name N or name CA or \ name C or name O or name CB )) or resid 1223 through 1228 or (resid 1229 and (n \ ame N or name CA or name C or name O or name CB )) or resid 1230 through 1232 or \ (resid 1233 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 234 or (resid 1235 through 1236 and (name N or name CA or name C or name O or na \ me CB )) or resid 1237 through 1238 or (resid 1239 through 1241 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1242 or (resid 1243 and (name \ N or name CA or name C or name O or name CB )) or resid 1244 through 1249 or (re \ sid 1250 and (name N or name CA or name C or name O or name CB )) or resid 1251 \ through 1258 or (resid 1259 through 1260 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1261 through 1264 or resid 4000)) selection = (chain 'B' and (resid 15 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 2 \ 3 through 30 or (resid 31 and (name N or name CA or name C or name O or name CB \ or name H or name HA or name HB2 or name HB3)) or resid 32 or (resid 33 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA or name HB2 o \ r name HB3)) or resid 34 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB or name CG or name H or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3)) or resid 53 through 64 or (resid 65 and (name N or name \ CA or name C or name O or name CB or name H or name HA or name HB2 or name HB3) \ ) or resid 66 through 68 or (resid 69 and (name N or name CA or name C or name O \ or name CB or name H or name HA or name HB2 or name HB3)) or resid 70 through 1 \ 53 or (resid 154 and (name N or name CA or name C or name O or name CB or name H \ or name HA or name HB2 or name HB3)) or resid 155 through 179 or (resid 180 and \ (name N or name CA or name C or name O or name CB or name H or name HA or name \ HB2 or name HB3)) or resid 181 through 192 or (resid 193 and (name N or name CA \ or name C or name O or name CB or name H or name HA or name HB2 or name HB3)) or \ resid 194 through 219 or (resid 220 and (name N or name CA or name C or name O \ or name CB or name CG or name SD or name CE )) or (resid 221 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name CE or name NZ ) \ ) or (resid 222 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name OD2)) or resid 223 through 242 or (resid 243 and (name N or \ name CA or name C or name O or name CB or name H or name HA or name HB2 or name \ HB3)) or resid 244 through 279 or (resid 280 and (name N or name CA or name C o \ r name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 281 \ through 284 or (resid 285 and (name N or name CA or name C or name O or name CB \ or name CG or name H or name HA or name HB2 or name HB3)) or (resid 286 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA or name HB2 o \ r name HB3)) or resid 287 through 288 or (resid 289 and (name N or name CA or na \ me C or name O or name CB or name OG1 or name CG2)) or resid 290 through 291 or \ (resid 292 through 293 and (name N or name CA or name C or name O or name CB or \ name H or name HA or name HB2 or name HB3)) or resid 294 through 303 or (resid 3 \ 04 and (name N or name CA or name C or name O or name CB or name H or name HA or \ name HB2 or name HB3)) or resid 305 through 306 or (resid 307 and (name N or na \ me CA or name C or name O or name CB or name H or name HA or name HB2 or name HB \ 3)) or resid 308 through 324 or (resid 325 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA or name HB2 or name HB3)) or resid 326 thr \ ough 334 or resid 422 or (resid 423 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name ND2)) or (resid 424 and (name N or name \ CA or name C or name O or name CB or name CG1 or name CG2 or name CD1)) or resi \ d 425 through 472 or (resid 473 and (name N or name CA or name C or name O or na \ me CB or name H or name HA or name HB2 or name HB3)) or resid 474 through 529 or \ (resid 530 through 531 and (name N or name CA or name C or name O or name CB or \ name H or name HA or name HB2 or name HB3)) or resid 532 through 533 or (resid \ 534 and (name N or name CA or name C or name O or name CB )) or resid 535 throug \ h 539 or (resid 540 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA or name HB2 or name HB3)) or resid 541 through 565 or (resid 566 \ and (name N or name CA or name C or name O or name CB or name H or name HA or na \ me HB2 or name HB3)) or resid 567 through 604 or resid 609 through 634 or (resid \ 635 and (name N or name CA or name C or name O or name CB or name H or name HA \ or name HB2 or name HB3)) or resid 636 through 663 or (resid 664 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2 or name H or name HA )) or resid 665 through 684 or resid 695 through 698 o \ r (resid 699 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name OE1 or name NE2)) or resid 700 through 723 or (resid 724 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or resid 725 or (r \ esid 726 and (name N or name CA or name C or name O or name CB )) or resid 727 t \ hrough 743 or (resid 744 and (name N or name CA or name C or name O or name CB o \ r name H or name HA or name HB2 or name HB3)) or resid 745 through 764 or (resid \ 765 and (name N or name CA or name C or name O or name CB )) or resid 766 throu \ gh 768 or (resid 769 and (name N or name CA or name C or name O or name CB or na \ me H or name HA or name HB2 or name HB3)) or resid 770 through 799 or (resid 800 \ and (name N or name CA or name C or name O or name CB or name H or name HA or n \ ame HB2 or name HB3)) or resid 801 through 806 or (resid 807 and (name N or name \ CA or name C or name O or name CB or name H or name HA or name HB2 or name HB3) \ ) or resid 808 through 814 or (resid 815 through 816 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA or name HB2 or name HB3)) or res \ id 817 through 830 or (resid 831 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA or name HB2 or name HB3)) or resid 832 through 833 o \ r (resid 834 through 835 and (name N or name CA or name C or name O or name CB o \ r name H or name HA or name HB2 or name HB3)) or resid 836 through 849 or (resid \ 850 through 851 and (name N or name CA or name C or name O or name CB or name H \ or name HA or name HB2 or name HB3)) or resid 852 through 872 or (resid 873 thr \ ough 875 and (name N or name CA or name C or name O or name CB or name H or name \ HA or name HB2 or name HB3)) or resid 876 through 882 or (resid 883 and (name N \ or name CA or name C or name O or name CB or name H or name HA or name HB2 or n \ ame HB3)) or resid 884 through 905 or (resid 906 and (name N or name CA or name \ C or name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 9 \ 07 through 923 or (resid 924 and (name N or name CA or name C or name O or name \ CB or name CG or name H or name HA or name HB2 or name HB3 or name HG2 or name H \ G3)) or resid 925 through 954 or (resid 955 and (name N or name CA or name C or \ name O or name CB or name H or name HA or name HB2 or name HB3)) or resid 956 th \ rough 1001 or (resid 1002 through 1003 and (name N or name CA or name C or name \ O or name CB or name OG1 or name CG2)) or resid 1004 through 1033 or (resid 1034 \ and (name N or name CA or name C or name O or name CB or name H or name HA or n \ ame HB2 or name HB3)) or (resid 1035 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA )) \ or resid 1036 through 1067 or (resid 1068 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2)) or resid 1069 through 1076 or (resid \ 1077 and (name N or name CA or name C or name O or name CB or name CG or name CD \ 1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or resid 1078 thr \ ough 1121 or (resid 1122 through 1123 and (name N or name CA or name C or name O \ or name CB )) or resid 1124 through 1150 or (resid 1151 and (name N or name CA \ or name C or name O or name CB )) or resid 1152 through 1185 or (resid 1186 and \ (name N or name CA or name C or name O or name CB )) or resid 1187 through 1206 \ or (resid 1207 and (name N or name CA or name C or name O or name CB )) or resid \ 1208 through 1216 or (resid 1217 and (name N or name CA or name C or name O or \ name CB )) or resid 1218 through 4000)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.560 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: 0.170 Extract box with map and model: 0.460 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.390 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.052 18782 Z= 0.101 Angle : 0.908 26.050 25651 Z= 0.476 Chirality : 0.174 1.733 2815 Planarity : 0.002 0.060 3346 Dihedral : 13.780 89.091 6607 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.76 % 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: -0.23 (0.18), residues: 2360 helix: 0.58 (0.39), residues: 218 sheet: -0.09 (0.23), residues: 570 loop : -0.22 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.011 0.001 TYR B1077 PHE 0.010 0.001 PHE B 470 TRP 0.010 0.001 TRP B 727 HIS 0.003 0.000 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00253 (18730) covalent geometry : angle 0.90869 (25559) SS BOND : bond 0.00145 ( 46) SS BOND : angle 0.54271 ( 92) hydrogen bonds : bond 0.23847 ( 475) hydrogen bonds : angle 8.69511 ( 1308) metal coordination : bond 0.00215 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 GLU cc_start: 0.5912 (mt-10) cc_final: 0.5681 (mt-10) REVERT: B 883 MET cc_start: 0.8201 (tpp) cc_final: 0.7852 (tpt) outliers start: 1 outliers final: 1 residues processed: 122 average time/residue: 0.3207 time to fit residues: 58.5615 Evaluate side-chains 98 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 263 GLN B 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.145726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.090092 restraints weight = 85276.660| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.03 r_work: 0.3149 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18782 Z= 0.217 Angle : 0.943 25.686 25651 Z= 0.498 Chirality : 0.175 1.757 2815 Planarity : 0.004 0.056 3346 Dihedral : 4.038 53.569 2547 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.35 % Allowed : 3.96 % Favored : 95.69 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 5.76 % 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: -0.40 (0.18), residues: 2360 helix: 0.71 (0.38), residues: 212 sheet: -0.12 (0.23), residues: 534 loop : -0.43 (0.17), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 574 TYR 0.020 0.001 TYR A1077 PHE 0.023 0.001 PHE B 236 TRP 0.009 0.001 TRP B 451 HIS 0.006 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00512 (18730) covalent geometry : angle 0.94443 (25559) SS BOND : bond 0.00306 ( 46) SS BOND : angle 0.62662 ( 92) hydrogen bonds : bond 0.04668 ( 475) hydrogen bonds : angle 6.49920 ( 1308) metal coordination : bond 0.00703 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 664 GLU cc_start: 0.5855 (mt-10) cc_final: 0.5636 (mt-10) REVERT: B 883 MET cc_start: 0.9055 (tpp) cc_final: 0.8461 (tpt) REVERT: C 137 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.8010 (ptm-80) outliers start: 7 outliers final: 6 residues processed: 98 average time/residue: 0.3461 time to fit residues: 50.0711 Evaluate side-chains 99 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain C residue 140 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 101 optimal weight: 30.0000 chunk 109 optimal weight: 0.2980 chunk 182 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.146180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.089700 restraints weight = 84517.536| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.34 r_work: 0.3214 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18782 Z= 0.147 Angle : 0.920 25.977 25651 Z= 0.483 Chirality : 0.174 1.745 2815 Planarity : 0.003 0.050 3346 Dihedral : 3.972 47.745 2547 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.41 % Allowed : 5.48 % Favored : 94.12 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.76 % 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: -0.47 (0.18), residues: 2360 helix: 0.83 (0.38), residues: 214 sheet: -0.32 (0.23), residues: 535 loop : -0.44 (0.17), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.011 0.001 TYR B 131 PHE 0.023 0.001 PHE B 236 TRP 0.008 0.001 TRP A1194 HIS 0.006 0.001 HIS B1050 Details of bonding type rmsd covalent geometry : bond 0.00355 (18730) covalent geometry : angle 0.92100 (25559) SS BOND : bond 0.00229 ( 46) SS BOND : angle 0.49776 ( 92) hydrogen bonds : bond 0.03802 ( 475) hydrogen bonds : angle 5.83803 ( 1308) metal coordination : bond 0.00311 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 TYR cc_start: 0.7513 (p90) cc_final: 0.7220 (p90) REVERT: B 883 MET cc_start: 0.9198 (tpp) cc_final: 0.8648 (tpt) REVERT: D 126 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7972 (tm-30) outliers start: 8 outliers final: 7 residues processed: 105 average time/residue: 0.3324 time to fit residues: 51.8844 Evaluate side-chains 101 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 143 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1154 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.146612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091390 restraints weight = 84046.696| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.72 r_work: 0.3186 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18782 Z= 0.148 Angle : 0.917 26.019 25651 Z= 0.482 Chirality : 0.174 1.729 2815 Planarity : 0.003 0.045 3346 Dihedral : 3.954 41.586 2547 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 0.51 % Allowed : 6.85 % Favored : 92.65 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 5.76 % 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: -0.49 (0.18), residues: 2360 helix: 0.98 (0.39), residues: 213 sheet: -0.34 (0.23), residues: 533 loop : -0.47 (0.17), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.014 0.001 TYR B1077 PHE 0.026 0.001 PHE B 236 TRP 0.007 0.001 TRP B 451 HIS 0.005 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00359 (18730) covalent geometry : angle 0.91840 (25559) SS BOND : bond 0.00214 ( 46) SS BOND : angle 0.49433 ( 92) hydrogen bonds : bond 0.03261 ( 475) hydrogen bonds : angle 5.37064 ( 1308) metal coordination : bond 0.00402 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 TYR cc_start: 0.7416 (p90) cc_final: 0.7126 (p90) REVERT: B 883 MET cc_start: 0.9033 (tpp) cc_final: 0.8466 (tpt) REVERT: C 137 ARG cc_start: 0.8413 (ptm-80) cc_final: 0.8063 (ptm-80) outliers start: 10 outliers final: 9 residues processed: 98 average time/residue: 0.3257 time to fit residues: 47.5822 Evaluate side-chains 99 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain C residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 176 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1050 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.146618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.090653 restraints weight = 84061.689| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.34 r_work: 0.3206 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18782 Z= 0.142 Angle : 0.915 26.029 25651 Z= 0.480 Chirality : 0.174 1.726 2815 Planarity : 0.003 0.044 3346 Dihedral : 3.920 35.064 2547 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.76 % Allowed : 8.06 % Favored : 91.18 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.76 % 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: -0.48 (0.18), residues: 2360 helix: 1.08 (0.39), residues: 213 sheet: -0.35 (0.22), residues: 542 loop : -0.48 (0.17), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.010 0.001 TYR B 131 PHE 0.025 0.001 PHE B 236 TRP 0.008 0.001 TRP B 842 HIS 0.005 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00347 (18730) covalent geometry : angle 0.91592 (25559) SS BOND : bond 0.00236 ( 46) SS BOND : angle 0.58403 ( 92) hydrogen bonds : bond 0.03131 ( 475) hydrogen bonds : angle 5.19794 ( 1308) metal coordination : bond 0.00372 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 TYR cc_start: 0.7512 (p90) cc_final: 0.7243 (p90) REVERT: B 883 MET cc_start: 0.9187 (tpp) cc_final: 0.8647 (tpt) REVERT: D 126 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 137 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.8056 (ptm-80) outliers start: 15 outliers final: 11 residues processed: 99 average time/residue: 0.3204 time to fit residues: 47.6653 Evaluate side-chains 102 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain D residue 143 SER Chi-restraints excluded: chain C residue 124 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 145 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 198 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.146141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.091997 restraints weight = 84009.303| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.88 r_work: 0.3164 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18782 Z= 0.164 Angle : 0.921 26.085 25651 Z= 0.483 Chirality : 0.174 1.729 2815 Planarity : 0.003 0.042 3346 Dihedral : 3.972 30.894 2547 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.66 % Allowed : 8.62 % Favored : 90.72 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.76 % 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: -0.51 (0.18), residues: 2360 helix: 1.07 (0.39), residues: 213 sheet: -0.36 (0.22), residues: 548 loop : -0.51 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.012 0.001 TYR B1077 PHE 0.026 0.001 PHE B 236 TRP 0.008 0.001 TRP B 451 HIS 0.007 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00396 (18730) covalent geometry : angle 0.92148 (25559) SS BOND : bond 0.00229 ( 46) SS BOND : angle 0.67104 ( 92) hydrogen bonds : bond 0.03162 ( 475) hydrogen bonds : angle 5.13547 ( 1308) metal coordination : bond 0.00455 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 TYR cc_start: 0.7495 (p90) cc_final: 0.7200 (p90) REVERT: B 883 MET cc_start: 0.8995 (tpp) cc_final: 0.8367 (tpt) REVERT: C 137 ARG cc_start: 0.8417 (ptm-80) cc_final: 0.8068 (ptm-80) outliers start: 13 outliers final: 11 residues processed: 100 average time/residue: 0.3215 time to fit residues: 48.1665 Evaluate side-chains 102 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain C residue 124 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 9 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 217 optimal weight: 0.7980 chunk 203 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.146723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092366 restraints weight = 83908.408| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.72 r_work: 0.3190 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18782 Z= 0.132 Angle : 0.913 26.038 25651 Z= 0.479 Chirality : 0.174 1.727 2815 Planarity : 0.003 0.042 3346 Dihedral : 3.865 18.523 2546 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.66 % Allowed : 9.28 % Favored : 90.06 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.76 % 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: -0.44 (0.18), residues: 2360 helix: 1.19 (0.39), residues: 213 sheet: -0.28 (0.22), residues: 553 loop : -0.48 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 574 TYR 0.011 0.001 TYR B 131 PHE 0.027 0.001 PHE B 236 TRP 0.008 0.001 TRP A 842 HIS 0.005 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00325 (18730) covalent geometry : angle 0.91361 (25559) SS BOND : bond 0.00191 ( 46) SS BOND : angle 0.57769 ( 92) hydrogen bonds : bond 0.02965 ( 475) hydrogen bonds : angle 5.01042 ( 1308) metal coordination : bond 0.00344 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 TYR cc_start: 0.7480 (p90) cc_final: 0.7170 (p90) REVERT: B 883 MET cc_start: 0.8995 (tpp) cc_final: 0.8428 (tpt) REVERT: D 126 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7944 (tm-30) REVERT: C 137 ARG cc_start: 0.8419 (ptm-80) cc_final: 0.8097 (ptm-80) outliers start: 13 outliers final: 13 residues processed: 102 average time/residue: 0.3014 time to fit residues: 46.0980 Evaluate side-chains 108 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain D residue 121 HIS Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain C residue 124 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 228 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.144277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093871 restraints weight = 83544.397| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.71 r_work: 0.3157 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 18782 Z= 0.255 Angle : 0.944 26.083 25651 Z= 0.497 Chirality : 0.175 1.735 2815 Planarity : 0.004 0.040 3346 Dihedral : 4.161 19.865 2546 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.76 % Allowed : 9.99 % Favored : 89.25 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.76 % 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: -0.67 (0.18), residues: 2360 helix: 0.88 (0.39), residues: 213 sheet: -0.33 (0.22), residues: 545 loop : -0.66 (0.17), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 574 TYR 0.015 0.001 TYR B1077 PHE 0.025 0.002 PHE B 236 TRP 0.011 0.001 TRP B 451 HIS 0.011 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00602 (18730) covalent geometry : angle 0.94477 (25559) SS BOND : bond 0.00313 ( 46) SS BOND : angle 0.71305 ( 92) hydrogen bonds : bond 0.03515 ( 475) hydrogen bonds : angle 5.20544 ( 1308) metal coordination : bond 0.00854 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 480 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7730 (tmt) REVERT: B 883 MET cc_start: 0.8980 (tpp) cc_final: 0.8353 (tpt) outliers start: 15 outliers final: 10 residues processed: 99 average time/residue: 0.3152 time to fit residues: 46.9510 Evaluate side-chains 100 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain C residue 124 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 37 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 102 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.146016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.091577 restraints weight = 83798.160| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.73 r_work: 0.3176 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18782 Z= 0.146 Angle : 0.918 26.011 25651 Z= 0.482 Chirality : 0.174 1.728 2815 Planarity : 0.003 0.043 3346 Dihedral : 4.018 18.947 2546 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.56 % Allowed : 10.40 % Favored : 89.05 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.76 % 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: -0.55 (0.18), residues: 2360 helix: 1.08 (0.39), residues: 213 sheet: -0.29 (0.23), residues: 529 loop : -0.58 (0.17), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.012 0.001 TYR B1077 PHE 0.025 0.001 PHE B 236 TRP 0.008 0.001 TRP B 73 HIS 0.007 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00353 (18730) covalent geometry : angle 0.91937 (25559) SS BOND : bond 0.00196 ( 46) SS BOND : angle 0.54485 ( 92) hydrogen bonds : bond 0.03045 ( 475) hydrogen bonds : angle 5.02528 ( 1308) metal coordination : bond 0.00387 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 883 MET cc_start: 0.8969 (tpp) cc_final: 0.8461 (tpt) REVERT: D 126 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7954 (tm-30) REVERT: C 137 ARG cc_start: 0.8446 (ptm-80) cc_final: 0.8140 (ptm-80) outliers start: 11 outliers final: 11 residues processed: 98 average time/residue: 0.3001 time to fit residues: 44.5574 Evaluate side-chains 103 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 300 HIS Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain C residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 1 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 80 optimal weight: 0.0270 chunk 10 optimal weight: 0.3980 chunk 164 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 231 optimal weight: 30.0000 chunk 54 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 overall best weight: 0.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.146339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.093813 restraints weight = 84510.175| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.60 r_work: 0.3197 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18782 Z= 0.127 Angle : 0.912 26.051 25651 Z= 0.479 Chirality : 0.174 1.726 2815 Planarity : 0.003 0.042 3346 Dihedral : 3.889 18.680 2546 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.51 % Allowed : 10.45 % Favored : 89.05 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.76 % 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: -0.50 (0.18), residues: 2360 helix: 1.02 (0.39), residues: 219 sheet: -0.38 (0.22), residues: 563 loop : -0.48 (0.17), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.011 0.001 TYR B 996 PHE 0.025 0.001 PHE B 236 TRP 0.007 0.001 TRP A 842 HIS 0.005 0.001 HIS B 78 Details of bonding type rmsd covalent geometry : bond 0.00314 (18730) covalent geometry : angle 0.91321 (25559) SS BOND : bond 0.00173 ( 46) SS BOND : angle 0.50943 ( 92) hydrogen bonds : bond 0.02864 ( 475) hydrogen bonds : angle 4.87781 ( 1308) metal coordination : bond 0.00330 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4720 Ramachandran restraints generated. 2360 Oldfield, 0 Emsley, 2360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 65 is missing expected H atoms. Skipping. Residue LYS 154 is missing expected H atoms. Skipping. Residue LYS 180 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue LEU 280 is missing expected H atoms. Skipping. Residue LYS 286 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 325 is missing expected H atoms. Skipping. Residue MET 473 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue LYS 530 is missing expected H atoms. Skipping. Residue SER 531 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 566 is missing expected H atoms. Skipping. Residue LYS 744 is missing expected H atoms. Skipping. Residue LYS 807 is missing expected H atoms. Skipping. Residue MET 816 is missing expected H atoms. Skipping. Residue MET 831 is missing expected H atoms. Skipping. Residue LEU 835 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue MET 883 is missing expected H atoms. Skipping. Residue LYS 1034 is missing expected H atoms. Skipping. Residue ILE 67 is missing expected H atoms. Skipping. Residue LYS 214 is missing expected H atoms. Skipping. Residue LYS 227 is missing expected H atoms. Skipping. Residue ALA 483 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 690 is missing expected H atoms. Skipping. Residue LEU 940 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 883 MET cc_start: 0.8965 (tpp) cc_final: 0.8437 (tpt) REVERT: D 126 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 137 ARG cc_start: 0.8468 (ptm-80) cc_final: 0.8111 (ptm-80) outliers start: 10 outliers final: 9 residues processed: 98 average time/residue: 0.2950 time to fit residues: 43.8725 Evaluate side-chains 100 residues out of total 2087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 811 ASP Chi-restraints excluded: chain D residue 135 ASP Chi-restraints excluded: chain C residue 124 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 45 optimal weight: 0.0770 chunk 221 optimal weight: 30.0000 chunk 166 optimal weight: 0.5980 chunk 198 optimal weight: 0.5980 chunk 157 optimal weight: 0.3980 chunk 184 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 226 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.147266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093528 restraints weight = 84049.602| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 3.74 r_work: 0.3207 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18782 Z= 0.102 Angle : 0.907 26.027 25651 Z= 0.476 Chirality : 0.174 1.729 2815 Planarity : 0.003 0.044 3346 Dihedral : 3.763 18.387 2546 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.51 % Allowed : 10.45 % Favored : 89.05 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.76 % 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: -0.40 (0.18), residues: 2360 helix: 1.18 (0.39), residues: 219 sheet: -0.32 (0.22), residues: 540 loop : -0.42 (0.17), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.011 0.001 TYR B 996 PHE 0.026 0.001 PHE B 236 TRP 0.007 0.001 TRP B 210 HIS 0.004 0.001 HIS A 78 Details of bonding type rmsd covalent geometry : bond 0.00257 (18730) covalent geometry : angle 0.90798 (25559) SS BOND : bond 0.00130 ( 46) SS BOND : angle 0.44389 ( 92) hydrogen bonds : bond 0.02650 ( 475) hydrogen bonds : angle 4.73824 ( 1308) metal coordination : bond 0.00218 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9345.57 seconds wall clock time: 159 minutes 8.84 seconds (9548.84 seconds total)