Starting phenix.real_space_refine on Thu Nov 20 04:24:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bcl_7082/11_2025/6bcl_7082.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bcl_7082/11_2025/6bcl_7082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bcl_7082/11_2025/6bcl_7082.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bcl_7082/11_2025/6bcl_7082.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bcl_7082/11_2025/6bcl_7082.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bcl_7082/11_2025/6bcl_7082.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 136 5.16 5 Na 2 4.78 5 C 19628 2.51 5 N 5340 2.21 5 O 5368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30474 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7618 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 37, 'TRANS': 929} Chain breaks: 8 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.01, per 1000 atoms: 0.23 Number of scatterers: 30474 At special positions: 0 Unit cell: (148.73, 148.73, 177.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 Na 2 11.00 O 5368 8.00 N 5340 7.00 C 19628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 989 " - pdb=" SG CYS B1007 " distance=2.03 Simple disulfide: pdb=" SG CYS A 989 " - pdb=" SG CYS A1007 " distance=2.03 Simple disulfide: pdb=" SG CYS C 989 " - pdb=" SG CYS C1007 " distance=2.03 Simple disulfide: pdb=" SG CYS D 989 " - pdb=" SG CYS D1007 " 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7232 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 12 sheets defined 66.9% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'B' and resid 14 through 19 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 284 through 295 removed outlier: 4.158A pdb=" N ARG B 288 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS B 311 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.738A pdb=" N LEU B 348 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU B 360 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 404 Processing helix chain 'B' and resid 406 through 415 removed outlier: 4.122A pdb=" N ALA B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 3.577A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 3.916A pdb=" N TYR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.678A pdb=" N ASN B 476 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 484 " --> pdb=" O GLN B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 558 through 569 removed outlier: 3.630A pdb=" N LEU B 562 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 582 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.574A pdb=" N LEU B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.563A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 670 through 681 Processing helix chain 'B' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 772 Processing helix chain 'B' and resid 774 through 799 Processing helix chain 'B' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 857 Processing helix chain 'B' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR B 880 " --> pdb=" O GLY B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS B 892 " --> pdb=" O ARG B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 906 removed outlier: 3.509A pdb=" N PHE B 906 " --> pdb=" O LEU B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 920 " --> pdb=" O ILE B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL B 926 " --> pdb=" O MET B 922 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 943 " --> pdb=" O ALA B 939 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 964 Processing helix chain 'B' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU B 968 " --> pdb=" O TYR B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 980 through 984 Processing helix chain 'B' and resid 1012 through 1029 removed outlier: 3.909A pdb=" N VAL B1016 " --> pdb=" O ALA B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1067 removed outlier: 5.778A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN B1049 " --> pdb=" O LYS B1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B1059 " --> pdb=" O LYS B1055 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B1060 " --> pdb=" O ALA B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1089 Processing helix chain 'B' and resid 1113 through 1141 Processing helix chain 'B' and resid 1142 through 1191 removed outlier: 4.486A pdb=" N GLN B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP B1168 " --> pdb=" O ILE B1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B1169 " --> pdb=" O ARG B1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B1170 " --> pdb=" O GLU B1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 19 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER A 178 " --> pdb=" O HIS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 284 through 295 removed outlier: 4.157A pdb=" N ARG A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.739A pdb=" N LEU A 348 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 removed outlier: 5.510A pdb=" N GLU A 360 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.637A pdb=" N ILE A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 406 through 415 removed outlier: 4.123A pdb=" N ALA A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 3.576A pdb=" N LEU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 removed outlier: 3.745A pdb=" N VAL A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.915A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.677A pdb=" N ASN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 484 " --> pdb=" O GLN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU A 562 " --> pdb=" O PRO A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 634 Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 670 through 681 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 703 removed outlier: 3.650A pdb=" N ILE A 703 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 774 through 799 Processing helix chain 'A' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 857 Processing helix chain 'A' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS A 892 " --> pdb=" O ARG A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 906 removed outlier: 3.510A pdb=" N PHE A 906 " --> pdb=" O LEU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER A 920 " --> pdb=" O ILE A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL A 926 " --> pdb=" O MET A 922 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 964 Processing helix chain 'A' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU A 968 " --> pdb=" O TYR A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 984 Processing helix chain 'A' and resid 1012 through 1029 removed outlier: 3.910A pdb=" N VAL A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR A1059 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER A1060 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1089 Processing helix chain 'A' and resid 1113 through 1141 Processing helix chain 'A' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A1164 " --> pdb=" O GLN A1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A1168 " --> pdb=" O ILE A1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A1169 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 284 through 295 removed outlier: 4.157A pdb=" N ARG C 288 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA C 295 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS C 311 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.738A pdb=" N LEU C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU C 360 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 406 through 415 removed outlier: 4.124A pdb=" N ALA C 410 " --> pdb=" O ARG C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 3.577A pdb=" N LEU C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.917A pdb=" N TYR C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 484 removed outlier: 3.678A pdb=" N ASN C 476 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 484 " --> pdb=" O GLN C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU C 562 " --> pdb=" O PRO C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 582 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 634 Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 670 through 681 Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.634A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE C 703 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 772 Processing helix chain 'C' and resid 774 through 799 Processing helix chain 'C' and resid 807 through 830 removed outlier: 3.561A pdb=" N LEU C 811 " --> pdb=" O SER C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 857 Processing helix chain 'C' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR C 880 " --> pdb=" O GLY C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 900 removed outlier: 4.030A pdb=" N CYS C 892 " --> pdb=" O ARG C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 906 removed outlier: 3.520A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER C 920 " --> pdb=" O ILE C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 948 removed outlier: 3.718A pdb=" N VAL C 926 " --> pdb=" O MET C 922 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA C 943 " --> pdb=" O ALA C 939 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C 948 " --> pdb=" O THR C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 954 through 964 Processing helix chain 'C' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU C 968 " --> pdb=" O TYR C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 984 Processing helix chain 'C' and resid 1012 through 1029 removed outlier: 3.911A pdb=" N VAL C1016 " --> pdb=" O ALA C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN C1049 " --> pdb=" O LYS C1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR C1059 " --> pdb=" O LYS C1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C1060 " --> pdb=" O ALA C1056 " (cutoff:3.500A) Processing helix chain 'C' and resid 1076 through 1089 Processing helix chain 'C' and resid 1113 through 1141 Processing helix chain 'C' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C1164 " --> pdb=" O GLN C1160 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C1168 " --> pdb=" O ILE C1164 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG C1169 " --> pdb=" O ARG C1165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C1170 " --> pdb=" O GLU C1166 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 163 through 178 removed outlier: 3.522A pdb=" N SER D 178 " --> pdb=" O HIS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 284 through 295 removed outlier: 4.158A pdb=" N ARG D 288 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 295 " --> pdb=" O ASP D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.354A pdb=" N CYS D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 344 through 356 removed outlier: 3.739A pdb=" N LEU D 348 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 362 removed outlier: 5.511A pdb=" N GLU D 360 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.636A pdb=" N ILE D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 406 through 415 removed outlier: 4.124A pdb=" N ALA D 410 " --> pdb=" O ARG D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 3.578A pdb=" N LEU D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 449 removed outlier: 3.744A pdb=" N VAL D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 removed outlier: 3.916A pdb=" N TYR D 465 " --> pdb=" O LEU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.677A pdb=" N ASN D 476 " --> pdb=" O SER D 472 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 484 " --> pdb=" O GLN D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 558 through 569 removed outlier: 3.629A pdb=" N LEU D 562 " --> pdb=" O PRO D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 582 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.573A pdb=" N LEU D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.562A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 670 through 681 Processing helix chain 'D' and resid 689 through 698 removed outlier: 3.633A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 703 removed outlier: 3.651A pdb=" N ILE D 703 " --> pdb=" O PRO D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 772 Processing helix chain 'D' and resid 774 through 799 Processing helix chain 'D' and resid 807 through 830 removed outlier: 3.562A pdb=" N LEU D 811 " --> pdb=" O SER D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 857 Processing helix chain 'D' and resid 859 through 880 removed outlier: 4.032A pdb=" N THR D 880 " --> pdb=" O GLY D 876 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 900 removed outlier: 4.029A pdb=" N CYS D 892 " --> pdb=" O ARG D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 906 Processing helix chain 'D' and resid 912 through 920 removed outlier: 4.012A pdb=" N VAL D 919 " --> pdb=" O LYS D 915 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER D 920 " --> pdb=" O ILE D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 948 removed outlier: 3.717A pdb=" N VAL D 926 " --> pdb=" O MET D 922 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 943 " --> pdb=" O ALA D 939 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 948 " --> pdb=" O THR D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 954 through 964 Processing helix chain 'D' and resid 964 through 970 removed outlier: 3.682A pdb=" N LEU D 968 " --> pdb=" O TYR D 964 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 984 Processing helix chain 'D' and resid 1012 through 1029 removed outlier: 3.911A pdb=" N VAL D1016 " --> pdb=" O ALA D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1029 through 1067 removed outlier: 5.778A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN D1049 " --> pdb=" O LYS D1045 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR D1059 " --> pdb=" O LYS D1055 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER D1060 " --> pdb=" O ALA D1056 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1089 Processing helix chain 'D' and resid 1113 through 1141 Processing helix chain 'D' and resid 1142 through 1191 removed outlier: 4.487A pdb=" N GLN D1163 " --> pdb=" O LYS D1159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP D1168 " --> pdb=" O ILE D1164 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG D1169 " --> pdb=" O ARG D1165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D1170 " --> pdb=" O GLU D1166 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.525A pdb=" N GLY B 77 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN B 90 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU B 235 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 92 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 237 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 94 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 186 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE B 234 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY B 188 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL B 236 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA B 190 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY B 157 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU B 300 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU B 276 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 302 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 278 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR B 365 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 301 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 985 through 986 removed outlier: 3.957A pdb=" N ILE B 985 " --> pdb=" O HIS B 998 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 21 through 23 Processing sheet with id=AA5, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY A 77 " --> pdb=" O PHE A 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN A 90 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 235 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 92 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP A 237 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 94 " --> pdb=" O ASP A 237 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 186 " --> pdb=" O ALA A 232 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE A 234 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY A 188 " --> pdb=" O PHE A 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL A 236 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA A 190 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY A 157 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU A 300 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU A 276 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 302 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU A 278 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N TYR A 365 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 301 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 985 through 986 removed outlier: 3.956A pdb=" N ILE A 985 " --> pdb=" O HIS A 998 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY C 77 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASN C 90 " --> pdb=" O PHE C 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU C 235 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU C 92 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP C 237 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 94 " --> pdb=" O ASP C 237 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA C 186 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE C 234 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 188 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL C 236 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA C 190 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY C 157 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU C 300 " --> pdb=" O VAL C 274 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU C 276 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL C 302 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU C 278 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N TYR C 365 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 301 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 985 through 986 removed outlier: 3.956A pdb=" N ILE C 985 " --> pdb=" O HIS C 998 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 79 removed outlier: 3.526A pdb=" N GLY D 77 " --> pdb=" O PHE D 91 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASN D 90 " --> pdb=" O PHE D 233 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU D 235 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU D 92 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASP D 237 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 94 " --> pdb=" O ASP D 237 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA D 186 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N PHE D 234 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY D 188 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL D 236 " --> pdb=" O GLY D 188 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA D 190 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLY D 157 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU D 300 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU D 276 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 302 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 278 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR D 365 " --> pdb=" O CYS D 299 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 301 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 985 through 986 removed outlier: 3.957A pdb=" N ILE D 985 " --> pdb=" O HIS D 998 " (cutoff:3.500A) 1779 hydrogen bonds defined for protein. 5265 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.92 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9880 1.34 - 1.46: 7411 1.46 - 1.58: 13649 1.58 - 1.71: 0 1.71 - 1.83: 204 Bond restraints: 31144 Sorted by residual: bond pdb=" C PRO C1073 " pdb=" N PRO C1074 " ideal model delta sigma weight residual 1.337 1.371 -0.034 1.11e-02 8.12e+03 9.52e+00 bond pdb=" C PRO A1073 " pdb=" N PRO A1074 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.11e-02 8.12e+03 9.20e+00 bond pdb=" C PRO D1073 " pdb=" N PRO D1074 " ideal model delta sigma weight residual 1.337 1.370 -0.034 1.11e-02 8.12e+03 9.13e+00 bond pdb=" C PRO B1073 " pdb=" N PRO B1074 " ideal model delta sigma weight residual 1.337 1.370 -0.033 1.11e-02 8.12e+03 8.88e+00 bond pdb=" C PHE C 340 " pdb=" N PRO C 341 " ideal model delta sigma weight residual 1.334 1.381 -0.048 2.34e-02 1.83e+03 4.13e+00 ... (remaining 31139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 40501 2.08 - 4.15: 1449 4.15 - 6.23: 201 6.23 - 8.30: 56 8.30 - 10.38: 25 Bond angle restraints: 42232 Sorted by residual: angle pdb=" N LEU B1030 " pdb=" CA LEU B1030 " pdb=" C LEU B1030 " ideal model delta sigma weight residual 111.36 118.54 -7.18 1.09e+00 8.42e-01 4.34e+01 angle pdb=" N ILE B1029 " pdb=" CA ILE B1029 " pdb=" C ILE B1029 " ideal model delta sigma weight residual 111.67 116.63 -4.96 9.50e-01 1.11e+00 2.72e+01 angle pdb=" N LEU C 948 " pdb=" CA LEU C 948 " pdb=" C LEU C 948 " ideal model delta sigma weight residual 108.41 100.41 8.00 1.63e+00 3.76e-01 2.41e+01 angle pdb=" N LEU A 948 " pdb=" CA LEU A 948 " pdb=" C LEU A 948 " ideal model delta sigma weight residual 108.41 100.44 7.97 1.63e+00 3.76e-01 2.39e+01 angle pdb=" N LEU B 948 " pdb=" CA LEU B 948 " pdb=" C LEU B 948 " ideal model delta sigma weight residual 108.41 100.47 7.94 1.63e+00 3.76e-01 2.37e+01 ... (remaining 42227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 17790 17.64 - 35.28: 588 35.28 - 52.93: 74 52.93 - 70.57: 8 70.57 - 88.21: 20 Dihedral angle restraints: 18480 sinusoidal: 7320 harmonic: 11160 Sorted by residual: dihedral pdb=" CB CYS D 989 " pdb=" SG CYS D 989 " pdb=" SG CYS D1007 " pdb=" CB CYS D1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.79 -88.21 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS A 989 " pdb=" SG CYS A 989 " pdb=" SG CYS A1007 " pdb=" CB CYS A1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.82 -88.18 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 989 " pdb=" SG CYS C 989 " pdb=" SG CYS C1007 " pdb=" CB CYS C1007 " ideal model delta sinusoidal sigma weight residual 93.00 -178.84 -88.16 1 1.00e+01 1.00e-02 9.29e+01 ... (remaining 18477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3508 0.057 - 0.113: 1152 0.113 - 0.170: 129 0.170 - 0.226: 2 0.226 - 0.283: 5 Chirality restraints: 4796 Sorted by residual: chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE D 279 " pdb=" CA ILE D 279 " pdb=" CG1 ILE D 279 " pdb=" CG2 ILE D 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CB ILE B 279 " pdb=" CA ILE B 279 " pdb=" CG1 ILE B 279 " pdb=" CG2 ILE B 279 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4793 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 816 " 0.024 2.00e-02 2.50e+03 2.03e-02 1.03e+01 pdb=" CG TRP D 816 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP D 816 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 816 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 816 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 816 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 816 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 816 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 816 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 816 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 816 " -0.025 2.00e-02 2.50e+03 2.02e-02 1.02e+01 pdb=" CG TRP A 816 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 816 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 816 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 816 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 816 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 816 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 816 " -0.024 2.00e-02 2.50e+03 2.01e-02 1.01e+01 pdb=" CG TRP B 816 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 816 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 816 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 816 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 816 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 816 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 816 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 816 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 816 " -0.002 2.00e-02 2.50e+03 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9732 2.84 - 3.35: 27498 3.35 - 3.87: 47502 3.87 - 4.38: 53447 4.38 - 4.90: 92626 Nonbonded interactions: 230805 Sorted by model distance: nonbonded pdb=" O ARG D 354 " pdb=" OG1 THR D 357 " model vdw 2.324 3.040 nonbonded pdb=" O ARG B 354 " pdb=" OG1 THR B 357 " model vdw 2.324 3.040 nonbonded pdb=" O ARG C 354 " pdb=" OG1 THR C 357 " model vdw 2.324 3.040 nonbonded pdb=" O ARG A 354 " pdb=" OG1 THR A 357 " model vdw 2.325 3.040 nonbonded pdb=" O VAL C 506 " pdb=" OG1 THR C 509 " model vdw 2.341 3.040 ... (remaining 230800 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 12 through 1193) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.630 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.008 0.055 31148 Z= 0.327 Angle : 0.963 10.380 42240 Z= 0.532 Chirality : 0.052 0.283 4796 Planarity : 0.006 0.064 5332 Dihedral : 9.609 76.901 11236 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.38 % Allowed : 2.00 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.83 (0.09), residues: 3796 helix: -3.23 (0.06), residues: 2408 sheet: -0.81 (0.37), residues: 208 loop : -3.13 (0.14), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 767 TYR 0.022 0.003 TYR B 339 PHE 0.024 0.003 PHE A 23 TRP 0.052 0.003 TRP D 816 HIS 0.007 0.003 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00751 (31144) covalent geometry : angle 0.96354 (42232) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.68990 ( 8) hydrogen bonds : bond 0.21930 ( 1779) hydrogen bonds : angle 7.72466 ( 5265) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 641 time to evaluate : 1.213 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 13 LYS cc_start: 0.2334 (OUTLIER) cc_final: 0.2098 (pmmt) REVERT: B 17 LYS cc_start: 0.8195 (ttpp) cc_final: 0.7743 (tptt) REVERT: B 173 ASP cc_start: 0.7735 (m-30) cc_final: 0.7130 (m-30) REVERT: B 197 ASN cc_start: 0.7270 (m-40) cc_final: 0.6541 (t0) REVERT: B 224 PHE cc_start: 0.6899 (m-10) cc_final: 0.6667 (m-10) REVERT: B 228 TYR cc_start: 0.7066 (p90) cc_final: 0.6673 (p90) REVERT: B 310 ASP cc_start: 0.7504 (t0) cc_final: 0.6867 (t0) REVERT: B 355 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6034 (mp) REVERT: B 356 MET cc_start: 0.7092 (mmm) cc_final: 0.6235 (tpp) REVERT: B 413 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 430 LEU cc_start: 0.8523 (tp) cc_final: 0.8194 (mt) REVERT: B 432 ASP cc_start: 0.7675 (m-30) cc_final: 0.7315 (m-30) REVERT: B 613 LYS cc_start: 0.8509 (mttt) cc_final: 0.8290 (mmmt) REVERT: B 675 LEU cc_start: 0.8717 (mt) cc_final: 0.8498 (tp) REVERT: B 695 LEU cc_start: 0.8805 (mt) cc_final: 0.8601 (mt) REVERT: B 825 LEU cc_start: 0.8228 (mp) cc_final: 0.7920 (pp) REVERT: B 873 LEU cc_start: 0.9172 (tp) cc_final: 0.8818 (tt) REVERT: B 979 MET cc_start: 0.9484 (ptt) cc_final: 0.9095 (ptm) REVERT: B 1145 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8077 (tm-30) REVERT: A 13 LYS cc_start: 0.2188 (OUTLIER) cc_final: 0.1943 (pmmt) REVERT: A 17 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7721 (tptt) REVERT: A 173 ASP cc_start: 0.7616 (m-30) cc_final: 0.7022 (m-30) REVERT: A 197 ASN cc_start: 0.7352 (m-40) cc_final: 0.7010 (t0) REVERT: A 224 PHE cc_start: 0.6915 (m-10) cc_final: 0.6674 (m-10) REVERT: A 228 TYR cc_start: 0.7045 (p90) cc_final: 0.6682 (p90) REVERT: A 310 ASP cc_start: 0.7508 (t0) cc_final: 0.6891 (t0) REVERT: A 355 ILE cc_start: 0.6297 (OUTLIER) cc_final: 0.5845 (mp) REVERT: A 356 MET cc_start: 0.7124 (mmm) cc_final: 0.6800 (tpp) REVERT: A 427 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7872 (mp0) REVERT: A 430 LEU cc_start: 0.8491 (tp) cc_final: 0.8122 (mt) REVERT: A 432 ASP cc_start: 0.7640 (m-30) cc_final: 0.7288 (m-30) REVERT: A 675 LEU cc_start: 0.8717 (mt) cc_final: 0.8440 (tp) REVERT: A 684 MET cc_start: 0.8659 (mtt) cc_final: 0.8442 (mtm) REVERT: A 695 LEU cc_start: 0.8895 (mt) cc_final: 0.8647 (mt) REVERT: A 823 GLU cc_start: 0.8212 (tp30) cc_final: 0.7865 (tp30) REVERT: A 825 LEU cc_start: 0.8296 (mp) cc_final: 0.7963 (pp) REVERT: A 873 LEU cc_start: 0.9186 (tp) cc_final: 0.8789 (tt) REVERT: A 1145 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8068 (tm-30) REVERT: C 13 LYS cc_start: 0.2301 (OUTLIER) cc_final: 0.2072 (pmmt) REVERT: C 17 LYS cc_start: 0.8146 (ttpp) cc_final: 0.7724 (tptt) REVERT: C 173 ASP cc_start: 0.7594 (m-30) cc_final: 0.7015 (m-30) REVERT: C 197 ASN cc_start: 0.7348 (m-40) cc_final: 0.7019 (t0) REVERT: C 224 PHE cc_start: 0.6935 (m-10) cc_final: 0.6691 (m-10) REVERT: C 228 TYR cc_start: 0.7021 (p90) cc_final: 0.6668 (p90) REVERT: C 310 ASP cc_start: 0.7507 (t0) cc_final: 0.6867 (t0) REVERT: C 355 ILE cc_start: 0.6348 (OUTLIER) cc_final: 0.5964 (mp) REVERT: C 356 MET cc_start: 0.7175 (mmm) cc_final: 0.6761 (tpp) REVERT: C 413 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 427 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7890 (mp0) REVERT: C 430 LEU cc_start: 0.8502 (tp) cc_final: 0.8119 (mt) REVERT: C 432 ASP cc_start: 0.7653 (m-30) cc_final: 0.7309 (m-30) REVERT: C 675 LEU cc_start: 0.8752 (mt) cc_final: 0.8507 (tp) REVERT: C 695 LEU cc_start: 0.8803 (mt) cc_final: 0.8565 (mt) REVERT: C 823 GLU cc_start: 0.8273 (tp30) cc_final: 0.7975 (tp30) REVERT: C 825 LEU cc_start: 0.8292 (mp) cc_final: 0.7966 (pp) REVERT: C 873 LEU cc_start: 0.9203 (tp) cc_final: 0.8815 (tt) REVERT: C 979 MET cc_start: 0.9397 (ptt) cc_final: 0.8864 (ptm) REVERT: C 1145 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8112 (tm-30) REVERT: D 16 ARG cc_start: 0.7513 (ptp-170) cc_final: 0.6870 (ptp-170) REVERT: D 17 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7881 (tptt) REVERT: D 163 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.6123 (pp) REVERT: D 169 VAL cc_start: 0.7215 (t) cc_final: 0.6821 (m) REVERT: D 173 ASP cc_start: 0.7608 (m-30) cc_final: 0.7191 (m-30) REVERT: D 197 ASN cc_start: 0.6730 (m-40) cc_final: 0.5995 (t0) REVERT: D 228 TYR cc_start: 0.7088 (p90) cc_final: 0.6649 (p90) REVERT: D 355 ILE cc_start: 0.6458 (OUTLIER) cc_final: 0.6147 (mp) REVERT: D 356 MET cc_start: 0.7075 (mmm) cc_final: 0.6552 (tpp) REVERT: D 413 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7486 (mt-10) REVERT: D 430 LEU cc_start: 0.8638 (tp) cc_final: 0.8243 (mt) REVERT: D 825 LEU cc_start: 0.8245 (mp) cc_final: 0.7951 (pp) REVERT: D 873 LEU cc_start: 0.9184 (tp) cc_final: 0.8829 (tt) REVERT: D 979 MET cc_start: 0.9440 (ptt) cc_final: 0.8962 (ptm) REVERT: D 1038 MET cc_start: 0.8864 (mtm) cc_final: 0.8633 (mtp) REVERT: D 1145 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8182 (tm-30) REVERT: D 1159 LYS cc_start: 0.8229 (mttt) cc_final: 0.7936 (tppt) outliers start: 12 outliers final: 0 residues processed: 653 average time/residue: 0.2548 time to fit residues: 242.7026 Evaluate side-chains 292 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 284 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN B 248 ASN B 261 GLN B 436 ASN B 476 ASN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 HIS A 136 GLN A 248 ASN A 261 GLN A 436 ASN A 476 ASN ** A 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 HIS C 136 GLN C 248 ASN C 261 GLN C 436 ASN C 476 ASN ** C 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 HIS D 136 GLN D 261 GLN D 436 ASN ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1080 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.133592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.102621 restraints weight = 65550.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.103714 restraints weight = 39024.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.103850 restraints weight = 27637.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104110 restraints weight = 27722.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104266 restraints weight = 25138.768| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31148 Z= 0.147 Angle : 0.602 7.565 42240 Z= 0.314 Chirality : 0.038 0.156 4796 Planarity : 0.005 0.051 5332 Dihedral : 5.278 59.461 4238 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.62 % Allowed : 7.06 % Favored : 91.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.12), residues: 3796 helix: -0.35 (0.09), residues: 2464 sheet: -1.00 (0.35), residues: 236 loop : -2.79 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 337 TYR 0.019 0.001 TYR C 339 PHE 0.031 0.002 PHE B 415 TRP 0.017 0.001 TRP D 214 HIS 0.004 0.001 HIS B 425 Details of bonding type rmsd covalent geometry : bond 0.00316 (31144) covalent geometry : angle 0.60183 (42232) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.11714 ( 8) hydrogen bonds : bond 0.05503 ( 1779) hydrogen bonds : angle 4.52237 ( 5265) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 362 time to evaluate : 1.189 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 16 ARG cc_start: 0.7245 (ptp-170) cc_final: 0.6885 (ptp-170) REVERT: B 17 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7865 (tptt) REVERT: B 197 ASN cc_start: 0.7119 (m-40) cc_final: 0.6807 (m-40) REVERT: B 355 ILE cc_start: 0.6600 (OUTLIER) cc_final: 0.6255 (mp) REVERT: B 356 MET cc_start: 0.7196 (mmm) cc_final: 0.6877 (tpp) REVERT: B 427 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: B 430 LEU cc_start: 0.8581 (tp) cc_final: 0.8309 (tp) REVERT: B 649 TRP cc_start: 0.6034 (OUTLIER) cc_final: 0.5614 (m-90) REVERT: B 977 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: B 979 MET cc_start: 0.9259 (ptt) cc_final: 0.8896 (ptm) REVERT: B 1119 LYS cc_start: 0.7769 (mtmt) cc_final: 0.7530 (mtmt) REVERT: A 16 ARG cc_start: 0.7324 (ptp-170) cc_final: 0.6924 (ptp-170) REVERT: A 17 LYS cc_start: 0.8333 (ttpp) cc_final: 0.7858 (tptt) REVERT: A 173 ASP cc_start: 0.7454 (m-30) cc_final: 0.7195 (m-30) REVERT: A 197 ASN cc_start: 0.7076 (m-40) cc_final: 0.6600 (t0) REVERT: A 355 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6260 (mp) REVERT: A 430 LEU cc_start: 0.8592 (tp) cc_final: 0.8331 (tp) REVERT: A 823 GLU cc_start: 0.8095 (tp30) cc_final: 0.7628 (tm-30) REVERT: A 825 LEU cc_start: 0.8045 (mp) cc_final: 0.7843 (pp) REVERT: A 979 MET cc_start: 0.9124 (ptt) cc_final: 0.8768 (ptt) REVERT: A 1119 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7545 (mtmt) REVERT: C 16 ARG cc_start: 0.7337 (ptp-170) cc_final: 0.6929 (ptp-170) REVERT: C 17 LYS cc_start: 0.8372 (ttpp) cc_final: 0.7904 (tptt) REVERT: C 173 ASP cc_start: 0.7457 (m-30) cc_final: 0.7256 (m-30) REVERT: C 197 ASN cc_start: 0.7204 (m-40) cc_final: 0.6701 (t0) REVERT: C 355 ILE cc_start: 0.6462 (OUTLIER) cc_final: 0.5925 (mp) REVERT: C 356 MET cc_start: 0.7213 (mmm) cc_final: 0.6861 (tpp) REVERT: C 430 LEU cc_start: 0.8603 (tp) cc_final: 0.8314 (tp) REVERT: C 823 GLU cc_start: 0.8191 (tp30) cc_final: 0.7717 (tm-30) REVERT: C 825 LEU cc_start: 0.8077 (mp) cc_final: 0.7876 (pp) REVERT: C 979 MET cc_start: 0.9148 (ptt) cc_final: 0.8723 (ptm) REVERT: D 17 LYS cc_start: 0.8402 (ttpp) cc_final: 0.8001 (tptt) REVERT: D 93 ARG cc_start: 0.7309 (ttt180) cc_final: 0.6871 (ttt90) REVERT: D 163 ILE cc_start: 0.6666 (OUTLIER) cc_final: 0.6464 (pp) REVERT: D 169 VAL cc_start: 0.7652 (t) cc_final: 0.7039 (m) REVERT: D 183 LYS cc_start: 0.6093 (mtpm) cc_final: 0.5536 (mtmm) REVERT: D 197 ASN cc_start: 0.6671 (m-40) cc_final: 0.6331 (t0) REVERT: D 355 ILE cc_start: 0.6610 (OUTLIER) cc_final: 0.6111 (mp) REVERT: D 356 MET cc_start: 0.7243 (mmm) cc_final: 0.6956 (tpp) REVERT: D 422 ARG cc_start: 0.5389 (tpp-160) cc_final: 0.5068 (tpp-160) REVERT: D 979 MET cc_start: 0.9187 (ptt) cc_final: 0.8776 (ptm) REVERT: D 1119 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7504 (mtmt) outliers start: 52 outliers final: 23 residues processed: 408 average time/residue: 0.2323 time to fit residues: 143.0175 Evaluate side-chains 296 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 785 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 166 optimal weight: 3.9990 chunk 217 optimal weight: 30.0000 chunk 23 optimal weight: 9.9990 chunk 244 optimal weight: 0.3980 chunk 255 optimal weight: 9.9990 chunk 311 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 382 optimal weight: 5.9990 chunk 340 optimal weight: 0.7980 chunk 304 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 633 ASN C 969 GLN ** C1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 969 GLN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.132983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102254 restraints weight = 66386.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103408 restraints weight = 43950.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103580 restraints weight = 30597.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.103851 restraints weight = 28385.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.103958 restraints weight = 25438.084| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 31148 Z= 0.126 Angle : 0.552 8.411 42240 Z= 0.283 Chirality : 0.038 0.158 4796 Planarity : 0.004 0.049 5332 Dihedral : 4.752 48.274 4238 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.59 % Allowed : 9.03 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.13), residues: 3796 helix: 0.94 (0.10), residues: 2484 sheet: -0.88 (0.36), residues: 228 loop : -2.62 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 140 TYR 0.023 0.001 TYR D 228 PHE 0.033 0.002 PHE C 415 TRP 0.014 0.001 TRP B1054 HIS 0.004 0.001 HIS D 174 Details of bonding type rmsd covalent geometry : bond 0.00277 (31144) covalent geometry : angle 0.55201 (42232) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.19521 ( 8) hydrogen bonds : bond 0.04538 ( 1779) hydrogen bonds : angle 4.01394 ( 5265) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 1.277 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 ARG cc_start: 0.7112 (ptp-170) cc_final: 0.6805 (ptp-170) REVERT: B 197 ASN cc_start: 0.6906 (m-40) cc_final: 0.6422 (t0) REVERT: B 356 MET cc_start: 0.7531 (mmm) cc_final: 0.7188 (tpp) REVERT: B 415 PHE cc_start: 0.6744 (m-80) cc_final: 0.6505 (m-80) REVERT: B 430 LEU cc_start: 0.8637 (tp) cc_final: 0.8303 (tp) REVERT: B 432 ASP cc_start: 0.7797 (t0) cc_final: 0.7587 (t0) REVERT: B 645 ARG cc_start: 0.7593 (mpt180) cc_final: 0.7349 (mpt180) REVERT: B 649 TRP cc_start: 0.6139 (OUTLIER) cc_final: 0.5771 (m-90) REVERT: B 977 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: B 979 MET cc_start: 0.9268 (ptt) cc_final: 0.8912 (ptm) REVERT: A 197 ASN cc_start: 0.6974 (m-40) cc_final: 0.6637 (m-40) REVERT: A 310 ASP cc_start: 0.6256 (t0) cc_final: 0.6025 (m-30) REVERT: A 427 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: A 823 GLU cc_start: 0.7865 (tp30) cc_final: 0.7545 (tm-30) REVERT: A 979 MET cc_start: 0.9219 (ptt) cc_final: 0.8830 (ptt) REVERT: C 173 ASP cc_start: 0.7484 (m-30) cc_final: 0.7278 (m-30) REVERT: C 197 ASN cc_start: 0.7047 (m-40) cc_final: 0.6717 (t0) REVERT: C 355 ILE cc_start: 0.6397 (OUTLIER) cc_final: 0.6142 (mp) REVERT: C 356 MET cc_start: 0.7533 (mmm) cc_final: 0.7272 (tpp) REVERT: C 427 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: C 432 ASP cc_start: 0.7774 (t0) cc_final: 0.7572 (t0) REVERT: C 823 GLU cc_start: 0.7906 (tp30) cc_final: 0.7561 (tm-30) REVERT: C 979 MET cc_start: 0.9248 (ptt) cc_final: 0.8876 (ptm) REVERT: D 16 ARG cc_start: 0.7189 (ptp-170) cc_final: 0.6892 (ptp-170) REVERT: D 17 LYS cc_start: 0.8356 (ttpp) cc_final: 0.7917 (tptt) REVERT: D 169 VAL cc_start: 0.7551 (t) cc_final: 0.7293 (m) REVERT: D 197 ASN cc_start: 0.6729 (m-40) cc_final: 0.6370 (t0) REVERT: D 355 ILE cc_start: 0.6581 (OUTLIER) cc_final: 0.6187 (mp) REVERT: D 464 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8490 (mt) REVERT: D 645 ARG cc_start: 0.7662 (mpt180) cc_final: 0.7455 (mpt180) REVERT: D 649 TRP cc_start: 0.6103 (OUTLIER) cc_final: 0.5624 (t-100) REVERT: D 979 MET cc_start: 0.9238 (ptt) cc_final: 0.8860 (ptm) outliers start: 51 outliers final: 25 residues processed: 353 average time/residue: 0.2275 time to fit residues: 122.7934 Evaluate side-chains 295 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 649 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 284 optimal weight: 0.9990 chunk 287 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 210 optimal weight: 30.0000 chunk 33 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 633 ASN ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 633 ASN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.130829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.100517 restraints weight = 65724.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101359 restraints weight = 46787.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101327 restraints weight = 36082.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101681 restraints weight = 33786.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101737 restraints weight = 31329.419| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31148 Z= 0.164 Angle : 0.576 7.220 42240 Z= 0.294 Chirality : 0.039 0.130 4796 Planarity : 0.004 0.050 5332 Dihedral : 4.524 55.234 4232 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.28 % Allowed : 9.62 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.31 (0.14), residues: 3796 helix: 1.42 (0.10), residues: 2484 sheet: -0.85 (0.36), residues: 232 loop : -2.50 (0.17), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 335 TYR 0.012 0.001 TYR B 967 PHE 0.026 0.002 PHE C 415 TRP 0.014 0.001 TRP D1054 HIS 0.005 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00378 (31144) covalent geometry : angle 0.57576 (42232) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.25882 ( 8) hydrogen bonds : bond 0.04880 ( 1779) hydrogen bonds : angle 3.99446 ( 5265) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 1.118 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 197 ASN cc_start: 0.6467 (m-40) cc_final: 0.6136 (t0) REVERT: B 351 GLN cc_start: 0.4976 (mm-40) cc_final: 0.4774 (mm-40) REVERT: B 356 MET cc_start: 0.7511 (mmm) cc_final: 0.7101 (tpp) REVERT: B 649 TRP cc_start: 0.6501 (OUTLIER) cc_final: 0.6130 (m-90) REVERT: B 1087 TRP cc_start: 0.5892 (t-100) cc_final: 0.5344 (t60) REVERT: A 156 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 197 ASN cc_start: 0.6896 (m-40) cc_final: 0.6463 (t0) REVERT: A 823 GLU cc_start: 0.7968 (tp30) cc_final: 0.7689 (tm-30) REVERT: A 979 MET cc_start: 0.9255 (ptt) cc_final: 0.8873 (ptt) REVERT: C 156 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8613 (p) REVERT: C 173 ASP cc_start: 0.7376 (m-30) cc_final: 0.7095 (m-30) REVERT: C 197 ASN cc_start: 0.7176 (m-40) cc_final: 0.6882 (m-40) REVERT: C 351 GLN cc_start: 0.4725 (mm-40) cc_final: 0.4171 (mm-40) REVERT: C 355 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6367 (mp) REVERT: C 356 MET cc_start: 0.7572 (mmm) cc_final: 0.7300 (tpp) REVERT: C 979 MET cc_start: 0.9312 (ptt) cc_final: 0.8862 (ptm) REVERT: C 1119 LYS cc_start: 0.7647 (mtmt) cc_final: 0.7385 (mtmt) REVERT: D 16 ARG cc_start: 0.7167 (ptp-170) cc_final: 0.6898 (ptp-170) REVERT: D 17 LYS cc_start: 0.8439 (ttpp) cc_final: 0.7990 (tptt) REVERT: D 156 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8228 (p) REVERT: D 163 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6639 (pp) REVERT: D 197 ASN cc_start: 0.6797 (m-40) cc_final: 0.6520 (m-40) REVERT: D 464 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8524 (mt) REVERT: D 645 ARG cc_start: 0.7820 (mpt180) cc_final: 0.7575 (mpt180) REVERT: D 1087 TRP cc_start: 0.5968 (t-100) cc_final: 0.5452 (t60) outliers start: 73 outliers final: 41 residues processed: 335 average time/residue: 0.2134 time to fit residues: 111.3801 Evaluate side-chains 299 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 250 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 649 TRP Chi-restraints excluded: chain C residue 659 MET Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1083 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 155 optimal weight: 1.9990 chunk 289 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 228 optimal weight: 8.9990 chunk 243 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 358 optimal weight: 0.0270 chunk 333 optimal weight: 0.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1013 ASN B1047 HIS A 782 ASN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 HIS C 782 ASN C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.099586 restraints weight = 66294.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099571 restraints weight = 47376.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099766 restraints weight = 39048.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100090 restraints weight = 35109.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100216 restraints weight = 31972.172| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31148 Z= 0.191 Angle : 0.605 8.102 42240 Z= 0.308 Chirality : 0.040 0.139 4796 Planarity : 0.004 0.049 5332 Dihedral : 4.487 45.670 4230 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.00 % Allowed : 10.12 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3796 helix: 1.56 (0.10), residues: 2488 sheet: -0.89 (0.35), residues: 232 loop : -2.39 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 337 TYR 0.011 0.001 TYR D 967 PHE 0.027 0.002 PHE B 415 TRP 0.014 0.002 TRP C 214 HIS 0.007 0.002 HIS C1127 Details of bonding type rmsd covalent geometry : bond 0.00447 (31144) covalent geometry : angle 0.60540 (42232) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.27884 ( 8) hydrogen bonds : bond 0.05122 ( 1779) hydrogen bonds : angle 4.07886 ( 5265) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 244 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 ASN cc_start: 0.6347 (m-40) cc_final: 0.5989 (t0) REVERT: B 351 GLN cc_start: 0.4979 (mm-40) cc_final: 0.4632 (mm-40) REVERT: B 356 MET cc_start: 0.7617 (mmm) cc_final: 0.7413 (tpp) REVERT: B 427 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: B 649 TRP cc_start: 0.6659 (OUTLIER) cc_final: 0.6207 (m-90) REVERT: B 662 ASP cc_start: 0.7932 (t0) cc_final: 0.7588 (t0) REVERT: B 979 MET cc_start: 0.9206 (ptt) cc_final: 0.8893 (ptt) REVERT: B 1051 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7789 (t0) REVERT: B 1087 TRP cc_start: 0.5883 (t-100) cc_final: 0.5380 (t60) REVERT: A 156 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8573 (p) REVERT: A 197 ASN cc_start: 0.6383 (m-40) cc_final: 0.6033 (t0) REVERT: A 351 GLN cc_start: 0.5054 (mm-40) cc_final: 0.4183 (mm-40) REVERT: A 427 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 430 LEU cc_start: 0.8680 (tp) cc_final: 0.8465 (tp) REVERT: A 662 ASP cc_start: 0.7975 (t0) cc_final: 0.7617 (t0) REVERT: C 156 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8579 (p) REVERT: C 173 ASP cc_start: 0.7384 (m-30) cc_final: 0.7069 (m-30) REVERT: C 197 ASN cc_start: 0.6454 (m-40) cc_final: 0.6080 (t0) REVERT: C 351 GLN cc_start: 0.4973 (mm-40) cc_final: 0.4502 (mm-40) REVERT: C 356 MET cc_start: 0.7739 (mmm) cc_final: 0.7424 (tpp) REVERT: C 427 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: C 430 LEU cc_start: 0.8678 (tp) cc_final: 0.8459 (tp) REVERT: C 649 TRP cc_start: 0.6269 (OUTLIER) cc_final: 0.6062 (t-100) REVERT: C 662 ASP cc_start: 0.7956 (t0) cc_final: 0.7602 (t0) REVERT: C 979 MET cc_start: 0.9333 (ptt) cc_final: 0.8903 (ptm) REVERT: C 1119 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7531 (mtmt) REVERT: C 1148 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8537 (mtpp) REVERT: D 156 THR cc_start: 0.8887 (OUTLIER) cc_final: 0.8413 (p) REVERT: D 197 ASN cc_start: 0.6501 (m-40) cc_final: 0.6230 (t0) REVERT: D 464 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8630 (mt) REVERT: D 1087 TRP cc_start: 0.5913 (t-100) cc_final: 0.5443 (t60) outliers start: 96 outliers final: 55 residues processed: 321 average time/residue: 0.2028 time to fit residues: 103.3890 Evaluate side-chains 302 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 236 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 649 TRP Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1083 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 331 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 302 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 375 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 782 ASN B1013 ASN A1013 ASN C1013 ASN C1047 HIS D 782 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.128155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098992 restraints weight = 66269.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.098381 restraints weight = 46850.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098960 restraints weight = 44727.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099158 restraints weight = 37063.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099411 restraints weight = 33644.945| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31148 Z= 0.229 Angle : 0.648 10.258 42240 Z= 0.329 Chirality : 0.042 0.209 4796 Planarity : 0.004 0.049 5332 Dihedral : 4.539 17.770 4228 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.06 % Allowed : 10.88 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.14), residues: 3796 helix: 1.54 (0.10), residues: 2468 sheet: -0.73 (0.36), residues: 212 loop : -2.31 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1118 TYR 0.013 0.001 TYR D 967 PHE 0.029 0.002 PHE D 415 TRP 0.016 0.002 TRP B 860 HIS 0.008 0.002 HIS B1127 Details of bonding type rmsd covalent geometry : bond 0.00539 (31144) covalent geometry : angle 0.64802 (42232) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.32503 ( 8) hydrogen bonds : bond 0.05507 ( 1779) hydrogen bonds : angle 4.23791 ( 5265) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 242 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: B 197 ASN cc_start: 0.6360 (m-40) cc_final: 0.6020 (t0) REVERT: B 351 GLN cc_start: 0.5204 (mm-40) cc_final: 0.4718 (mm-40) REVERT: B 427 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: B 430 LEU cc_start: 0.8659 (tp) cc_final: 0.8446 (tp) REVERT: B 662 ASP cc_start: 0.7952 (t0) cc_final: 0.7619 (t0) REVERT: B 1076 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8083 (tt) REVERT: B 1087 TRP cc_start: 0.5927 (t-100) cc_final: 0.5423 (t60) REVERT: A 197 ASN cc_start: 0.6382 (m-40) cc_final: 0.6141 (t0) REVERT: A 351 GLN cc_start: 0.5110 (mm-40) cc_final: 0.4203 (mm-40) REVERT: A 427 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 431 MET cc_start: 0.8643 (tpp) cc_final: 0.8434 (tpp) REVERT: A 649 TRP cc_start: 0.6378 (OUTLIER) cc_final: 0.5925 (t-100) REVERT: A 662 ASP cc_start: 0.7912 (t0) cc_final: 0.7593 (t0) REVERT: A 1030 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8319 (mp) REVERT: C 173 ASP cc_start: 0.7433 (m-30) cc_final: 0.7110 (m-30) REVERT: C 197 ASN cc_start: 0.6380 (m-40) cc_final: 0.6037 (t0) REVERT: C 351 GLN cc_start: 0.5203 (mm-40) cc_final: 0.4584 (mm-40) REVERT: C 356 MET cc_start: 0.7702 (mmm) cc_final: 0.7200 (tpp) REVERT: C 427 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: C 649 TRP cc_start: 0.6393 (OUTLIER) cc_final: 0.5909 (t-100) REVERT: C 979 MET cc_start: 0.9317 (ptt) cc_final: 0.8885 (ptm) REVERT: C 1030 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8281 (mp) REVERT: C 1148 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8562 (mtpp) REVERT: D 163 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6520 (pp) REVERT: D 197 ASN cc_start: 0.6448 (m-40) cc_final: 0.6247 (t0) REVERT: D 1076 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8055 (tt) REVERT: D 1087 TRP cc_start: 0.5956 (t-100) cc_final: 0.5446 (t60) outliers start: 98 outliers final: 63 residues processed: 321 average time/residue: 0.2133 time to fit residues: 109.2194 Evaluate side-chains 301 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 227 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 977 GLU Chi-restraints excluded: chain B residue 1013 ASN Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1083 LEU Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 649 TRP Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1013 ASN Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 649 TRP Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1083 LEU Chi-restraints excluded: chain C residue 1148 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 785 SER Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1076 ILE Chi-restraints excluded: chain D residue 1083 LEU Chi-restraints excluded: chain D residue 1144 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 263 optimal weight: 0.9990 chunk 174 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101312 restraints weight = 66243.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102685 restraints weight = 46813.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102722 restraints weight = 32025.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102953 restraints weight = 30546.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102939 restraints weight = 28097.610| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 31148 Z= 0.114 Angle : 0.542 12.591 42240 Z= 0.273 Chirality : 0.038 0.195 4796 Planarity : 0.004 0.047 5332 Dihedral : 4.175 17.716 4228 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.06 % Allowed : 12.34 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.14), residues: 3796 helix: 1.87 (0.10), residues: 2496 sheet: -0.61 (0.36), residues: 212 loop : -2.23 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1118 TYR 0.011 0.001 TYR A 339 PHE 0.029 0.001 PHE A 91 TRP 0.014 0.001 TRP D1123 HIS 0.004 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00248 (31144) covalent geometry : angle 0.54233 (42232) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.07389 ( 8) hydrogen bonds : bond 0.04037 ( 1779) hydrogen bonds : angle 3.84692 ( 5265) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 264 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 THR cc_start: 0.8686 (m) cc_final: 0.8246 (p) REVERT: B 197 ASN cc_start: 0.6355 (m-40) cc_final: 0.6154 (t0) REVERT: B 351 GLN cc_start: 0.5016 (mm-40) cc_final: 0.4609 (mm-40) REVERT: B 427 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7313 (mp0) REVERT: B 430 LEU cc_start: 0.8542 (tp) cc_final: 0.8101 (mt) REVERT: B 431 MET cc_start: 0.8691 (tpp) cc_final: 0.8451 (tpp) REVERT: B 649 TRP cc_start: 0.6625 (OUTLIER) cc_final: 0.6194 (m-90) REVERT: B 662 ASP cc_start: 0.7849 (t0) cc_final: 0.7541 (t0) REVERT: B 979 MET cc_start: 0.9110 (ptt) cc_final: 0.8760 (ptt) REVERT: B 1076 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7806 (tt) REVERT: B 1087 TRP cc_start: 0.5857 (t-100) cc_final: 0.5357 (t60) REVERT: A 156 THR cc_start: 0.8717 (m) cc_final: 0.8326 (p) REVERT: A 351 GLN cc_start: 0.5073 (mm-40) cc_final: 0.4229 (mm-40) REVERT: A 427 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: A 430 LEU cc_start: 0.8540 (tp) cc_final: 0.8161 (mt) REVERT: A 431 MET cc_start: 0.8681 (tpp) cc_final: 0.8460 (tpp) REVERT: A 662 ASP cc_start: 0.7865 (t0) cc_final: 0.7547 (t0) REVERT: C 156 THR cc_start: 0.8671 (m) cc_final: 0.8405 (p) REVERT: C 173 ASP cc_start: 0.7396 (m-30) cc_final: 0.7105 (m-30) REVERT: C 197 ASN cc_start: 0.6375 (m-40) cc_final: 0.6143 (t0) REVERT: C 351 GLN cc_start: 0.5201 (mm-40) cc_final: 0.4648 (mm-40) REVERT: C 356 MET cc_start: 0.7590 (mmm) cc_final: 0.7095 (tpp) REVERT: C 427 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: C 430 LEU cc_start: 0.8549 (tp) cc_final: 0.8194 (mt) REVERT: C 979 MET cc_start: 0.9270 (ptt) cc_final: 0.8846 (ptt) REVERT: D 17 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7811 (tptt) REVERT: D 156 THR cc_start: 0.8701 (m) cc_final: 0.8300 (p) REVERT: D 430 LEU cc_start: 0.8582 (tp) cc_final: 0.8243 (mt) REVERT: D 1076 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7824 (tt) REVERT: D 1087 TRP cc_start: 0.5878 (t-100) cc_final: 0.5387 (t60) outliers start: 66 outliers final: 37 residues processed: 318 average time/residue: 0.2059 time to fit residues: 104.3526 Evaluate side-chains 285 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 242 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1076 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 152 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 379 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 317 optimal weight: 7.9990 chunk 320 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 284 optimal weight: 0.9980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN ** D1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.128940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.100013 restraints weight = 66734.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.098915 restraints weight = 46421.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.099505 restraints weight = 45207.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.099920 restraints weight = 36877.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.100127 restraints weight = 33821.207| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 31148 Z= 0.195 Angle : 0.614 12.979 42240 Z= 0.309 Chirality : 0.041 0.139 4796 Planarity : 0.004 0.048 5332 Dihedral : 4.331 16.895 4228 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.00 % Allowed : 12.84 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3796 helix: 1.84 (0.10), residues: 2464 sheet: -0.59 (0.36), residues: 212 loop : -2.23 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1118 TYR 0.012 0.001 TYR C 967 PHE 0.028 0.002 PHE D 91 TRP 0.015 0.001 TRP A 860 HIS 0.007 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00457 (31144) covalent geometry : angle 0.61451 (42232) SS BOND : bond 0.00233 ( 4) SS BOND : angle 0.28836 ( 8) hydrogen bonds : bond 0.05044 ( 1779) hydrogen bonds : angle 4.08609 ( 5265) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 233 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: B 197 ASN cc_start: 0.6366 (m-40) cc_final: 0.6047 (t0) REVERT: B 351 GLN cc_start: 0.5176 (mm-40) cc_final: 0.4644 (mm-40) REVERT: B 427 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: B 430 LEU cc_start: 0.8619 (tp) cc_final: 0.8368 (mt) REVERT: B 431 MET cc_start: 0.8665 (tpp) cc_final: 0.8441 (tpp) REVERT: B 649 TRP cc_start: 0.6657 (OUTLIER) cc_final: 0.6222 (m-90) REVERT: B 662 ASP cc_start: 0.7946 (t0) cc_final: 0.7615 (t0) REVERT: B 1076 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8075 (tt) REVERT: B 1087 TRP cc_start: 0.5938 (t-100) cc_final: 0.5442 (t60) REVERT: A 351 GLN cc_start: 0.5135 (mm-40) cc_final: 0.4230 (mm-40) REVERT: A 427 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: A 430 LEU cc_start: 0.8608 (tp) cc_final: 0.8392 (tp) REVERT: A 431 MET cc_start: 0.8649 (tpp) cc_final: 0.8415 (tpp) REVERT: A 662 ASP cc_start: 0.7992 (t0) cc_final: 0.7677 (t0) REVERT: C 173 ASP cc_start: 0.7394 (m-30) cc_final: 0.7076 (m-30) REVERT: C 197 ASN cc_start: 0.6409 (m-40) cc_final: 0.6173 (t0) REVERT: C 351 GLN cc_start: 0.5194 (mm-40) cc_final: 0.4520 (mm-40) REVERT: C 356 MET cc_start: 0.7824 (mmm) cc_final: 0.7341 (tpp) REVERT: C 427 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: C 430 LEU cc_start: 0.8617 (tp) cc_final: 0.8224 (mt) REVERT: C 662 ASP cc_start: 0.8009 (t0) cc_final: 0.7642 (t0) REVERT: C 979 MET cc_start: 0.9264 (ptt) cc_final: 0.8849 (ptt) REVERT: D 163 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6545 (pp) REVERT: D 430 LEU cc_start: 0.8621 (tp) cc_final: 0.8364 (tp) REVERT: D 662 ASP cc_start: 0.7988 (t0) cc_final: 0.7621 (t0) REVERT: D 979 MET cc_start: 0.9211 (ptt) cc_final: 0.8847 (ptt) REVERT: D 1087 TRP cc_start: 0.5953 (t-100) cc_final: 0.5470 (t60) outliers start: 64 outliers final: 49 residues processed: 280 average time/residue: 0.2102 time to fit residues: 93.5347 Evaluate side-chains 286 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain B residue 1144 SER Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain C residue 1144 SER Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 873 LEU Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1144 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 315 optimal weight: 1.9990 chunk 64 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 chunk 271 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 GLN ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.131161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101151 restraints weight = 66257.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.101829 restraints weight = 48334.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.102055 restraints weight = 36162.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102294 restraints weight = 32825.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102371 restraints weight = 30755.089| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31148 Z= 0.120 Angle : 0.547 13.884 42240 Z= 0.274 Chirality : 0.038 0.245 4796 Planarity : 0.003 0.046 5332 Dihedral : 4.131 16.021 4228 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.81 % Allowed : 13.25 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.14), residues: 3796 helix: 2.05 (0.10), residues: 2464 sheet: -0.44 (0.36), residues: 212 loop : -2.20 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1118 TYR 0.011 0.001 TYR A 339 PHE 0.028 0.001 PHE D 91 TRP 0.013 0.001 TRP D1123 HIS 0.006 0.001 HIS C1127 Details of bonding type rmsd covalent geometry : bond 0.00267 (31144) covalent geometry : angle 0.54738 (42232) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.19897 ( 8) hydrogen bonds : bond 0.04108 ( 1779) hydrogen bonds : angle 3.85410 ( 5265) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 245 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 156 THR cc_start: 0.8753 (m) cc_final: 0.8393 (p) REVERT: B 197 ASN cc_start: 0.6358 (m-40) cc_final: 0.6121 (t0) REVERT: B 351 GLN cc_start: 0.5074 (mm-40) cc_final: 0.4630 (mm-40) REVERT: B 427 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: B 430 LEU cc_start: 0.8585 (tp) cc_final: 0.8337 (mt) REVERT: B 431 MET cc_start: 0.8707 (tpp) cc_final: 0.8495 (tpp) REVERT: B 649 TRP cc_start: 0.6595 (OUTLIER) cc_final: 0.6191 (m-90) REVERT: B 662 ASP cc_start: 0.7871 (t0) cc_final: 0.7576 (t0) REVERT: B 1076 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7855 (tt) REVERT: B 1087 TRP cc_start: 0.5868 (t-100) cc_final: 0.5380 (t60) REVERT: A 156 THR cc_start: 0.8745 (m) cc_final: 0.8371 (p) REVERT: A 351 GLN cc_start: 0.5177 (mm-40) cc_final: 0.4335 (mm-40) REVERT: A 427 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: A 430 LEU cc_start: 0.8582 (tp) cc_final: 0.8210 (mt) REVERT: A 431 MET cc_start: 0.8675 (tpp) cc_final: 0.8453 (tpp) REVERT: A 662 ASP cc_start: 0.7903 (t0) cc_final: 0.7592 (t0) REVERT: A 1030 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8201 (mp) REVERT: C 156 THR cc_start: 0.8687 (m) cc_final: 0.8390 (p) REVERT: C 173 ASP cc_start: 0.7413 (m-30) cc_final: 0.7112 (m-30) REVERT: C 197 ASN cc_start: 0.6365 (m-40) cc_final: 0.6129 (t0) REVERT: C 351 GLN cc_start: 0.5308 (mm-40) cc_final: 0.4708 (mm-40) REVERT: C 356 MET cc_start: 0.7751 (mmm) cc_final: 0.7221 (tpp) REVERT: C 427 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: C 430 LEU cc_start: 0.8574 (tp) cc_final: 0.8177 (mt) REVERT: C 662 ASP cc_start: 0.7842 (t0) cc_final: 0.7478 (t0) REVERT: C 979 MET cc_start: 0.9255 (ptt) cc_final: 0.8822 (ptt) REVERT: C 1030 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8211 (mp) REVERT: D 156 THR cc_start: 0.8723 (m) cc_final: 0.8265 (p) REVERT: D 163 ILE cc_start: 0.6754 (OUTLIER) cc_final: 0.6363 (pp) REVERT: D 430 LEU cc_start: 0.8554 (tp) cc_final: 0.8320 (tp) REVERT: D 662 ASP cc_start: 0.7829 (t0) cc_final: 0.7464 (t0) REVERT: D 1087 TRP cc_start: 0.6032 (t-100) cc_final: 0.5456 (t60) outliers start: 58 outliers final: 42 residues processed: 290 average time/residue: 0.2122 time to fit residues: 97.6642 Evaluate side-chains 288 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 238 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 785 SER Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 176 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 350 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 220 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.130766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.100779 restraints weight = 66016.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.101730 restraints weight = 45181.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.101714 restraints weight = 35406.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.101985 restraints weight = 32997.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102049 restraints weight = 30234.343| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31148 Z= 0.133 Angle : 0.563 13.927 42240 Z= 0.281 Chirality : 0.039 0.252 4796 Planarity : 0.004 0.046 5332 Dihedral : 4.081 15.764 4228 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.66 % Allowed : 13.41 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.14), residues: 3796 helix: 2.09 (0.10), residues: 2468 sheet: -0.31 (0.36), residues: 212 loop : -2.21 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1118 TYR 0.011 0.001 TYR A 339 PHE 0.033 0.001 PHE A 91 TRP 0.015 0.001 TRP A 214 HIS 0.006 0.001 HIS A1127 Details of bonding type rmsd covalent geometry : bond 0.00303 (31144) covalent geometry : angle 0.56286 (42232) SS BOND : bond 0.00152 ( 4) SS BOND : angle 0.18327 ( 8) hydrogen bonds : bond 0.04256 ( 1779) hydrogen bonds : angle 3.86272 ( 5265) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7592 Ramachandran restraints generated. 3796 Oldfield, 0 Emsley, 3796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 238 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 156 THR cc_start: 0.8732 (m) cc_final: 0.8361 (p) REVERT: B 197 ASN cc_start: 0.6363 (m-40) cc_final: 0.6123 (t0) REVERT: B 351 GLN cc_start: 0.5172 (mm-40) cc_final: 0.4687 (mm-40) REVERT: B 427 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: B 430 LEU cc_start: 0.8594 (tp) cc_final: 0.8348 (mt) REVERT: B 649 TRP cc_start: 0.6561 (OUTLIER) cc_final: 0.6165 (m-90) REVERT: B 662 ASP cc_start: 0.7885 (t0) cc_final: 0.7599 (t0) REVERT: B 979 MET cc_start: 0.9147 (ptt) cc_final: 0.8819 (ptt) REVERT: B 1076 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7882 (tt) REVERT: B 1087 TRP cc_start: 0.5953 (t-100) cc_final: 0.5404 (t60) REVERT: A 156 THR cc_start: 0.8783 (m) cc_final: 0.8415 (p) REVERT: A 351 GLN cc_start: 0.5229 (mm-40) cc_final: 0.4362 (mm-40) REVERT: A 427 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: A 430 LEU cc_start: 0.8594 (tp) cc_final: 0.8219 (mt) REVERT: A 431 MET cc_start: 0.8719 (tpp) cc_final: 0.8513 (tpp) REVERT: A 662 ASP cc_start: 0.7904 (t0) cc_final: 0.7603 (t0) REVERT: A 1030 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8284 (mp) REVERT: C 156 THR cc_start: 0.8759 (m) cc_final: 0.8399 (p) REVERT: C 173 ASP cc_start: 0.7391 (m-30) cc_final: 0.7083 (m-30) REVERT: C 197 ASN cc_start: 0.6365 (m-40) cc_final: 0.6132 (t0) REVERT: C 351 GLN cc_start: 0.5319 (mm-40) cc_final: 0.4698 (mm-40) REVERT: C 356 MET cc_start: 0.7809 (mmm) cc_final: 0.7198 (tpp) REVERT: C 427 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: C 430 LEU cc_start: 0.8609 (tp) cc_final: 0.8203 (mt) REVERT: C 431 MET cc_start: 0.8659 (tpp) cc_final: 0.8399 (tpp) REVERT: C 662 ASP cc_start: 0.7928 (t0) cc_final: 0.7554 (t0) REVERT: C 979 MET cc_start: 0.9261 (ptt) cc_final: 0.8821 (ptt) REVERT: C 1030 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8285 (mp) REVERT: D 156 THR cc_start: 0.8714 (m) cc_final: 0.8219 (p) REVERT: D 163 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6389 (pp) REVERT: D 431 MET cc_start: 0.8699 (tpp) cc_final: 0.8436 (tpp) REVERT: D 662 ASP cc_start: 0.7891 (t0) cc_final: 0.7523 (t0) REVERT: D 979 MET cc_start: 0.9212 (ptt) cc_final: 0.8865 (ptt) REVERT: D 1087 TRP cc_start: 0.6032 (t-100) cc_final: 0.5466 (t60) outliers start: 53 outliers final: 45 residues processed: 278 average time/residue: 0.2065 time to fit residues: 92.0209 Evaluate side-chains 290 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 LYS Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 427 GLU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 649 TRP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 1051 ASP Chi-restraints excluded: chain B residue 1076 ILE Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 1030 LEU Chi-restraints excluded: chain A residue 1051 ASP Chi-restraints excluded: chain C residue 13 LYS Chi-restraints excluded: chain C residue 117 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 457 THR Chi-restraints excluded: chain C residue 560 SER Chi-restraints excluded: chain C residue 770 ASP Chi-restraints excluded: chain C residue 785 SER Chi-restraints excluded: chain C residue 894 ASP Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 1013 ASN Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1051 ASP Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 457 THR Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 770 ASP Chi-restraints excluded: chain D residue 937 LEU Chi-restraints excluded: chain D residue 1013 ASN Chi-restraints excluded: chain D residue 1051 ASP Chi-restraints excluded: chain D residue 1084 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 110 optimal weight: 0.4980 chunk 94 optimal weight: 0.6980 chunk 19 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 377 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 GLN ** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1013 ASN ** D 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.132003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.101740 restraints weight = 66502.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103238 restraints weight = 46321.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.103101 restraints weight = 33408.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103347 restraints weight = 30644.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103335 restraints weight = 28262.115| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31148 Z= 0.112 Angle : 0.544 14.154 42240 Z= 0.271 Chirality : 0.038 0.252 4796 Planarity : 0.003 0.045 5332 Dihedral : 4.002 16.180 4228 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.84 % Allowed : 13.34 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.14), residues: 3796 helix: 2.21 (0.10), residues: 2472 sheet: -0.11 (0.36), residues: 208 loop : -2.16 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1118 TYR 0.011 0.001 TYR A 339 PHE 0.032 0.001 PHE A 91 TRP 0.013 0.001 TRP D1123 HIS 0.005 0.001 HIS B1127 Details of bonding type rmsd covalent geometry : bond 0.00247 (31144) covalent geometry : angle 0.54359 (42232) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.11503 ( 8) hydrogen bonds : bond 0.03867 ( 1779) hydrogen bonds : angle 3.75511 ( 5265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4746.96 seconds wall clock time: 82 minutes 42.00 seconds (4962.00 seconds total)