Starting phenix.real_space_refine on Mon Apr 6 18:20:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x2b_22000/04_2026/6x2b_22000_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x2b_22000/04_2026/6x2b_22000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x2b_22000/04_2026/6x2b_22000.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x2b_22000/04_2026/6x2b_22000.map" model { file = "/net/cci-nas-00/data/ceres_data/6x2b_22000/04_2026/6x2b_22000_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x2b_22000/04_2026/6x2b_22000_neut.cif" } resolution = 3.6 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= 0.003 sd= 0.048 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: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 13483 2.51 5 N 3554 2.21 5 O 3988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21120 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 963, 7380 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 47, 'TRANS': 915} Chain breaks: 12 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 5, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 10, 'TYR:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 6870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6870 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Chain: "C" Number of atoms: 6870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6870 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ASP:plan': 13, 'ASN:plan1': 17, 'GLU:plan': 12, 'GLN:plan1': 9, 'ARG:plan': 9, 'PHE:plan': 9, 'TYR:plan': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 382 Time building chain proxies: 4.72, per 1000 atoms: 0.22 Number of scatterers: 21120 At special positions: 0 Unit cell: (128.018, 132.25, 178.802, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 3988 8.00 N 3554 7.00 C 13483 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 931.1 milliseconds 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 44 sheets defined 27.6% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.062A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.842A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.334A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.247A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 759 removed outlier: 7.224A pdb=" N SER A 758 " --> pdb=" O GLN A 755 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 759 " --> pdb=" O TYR A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 760 through 783 removed outlier: 3.969A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.628A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 4.023A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.689A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.571A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.500A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.543A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.854A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.988A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.533A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.248A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.799A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.943A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.238A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 759 removed outlier: 7.311A pdb=" N SER B 758 " --> pdb=" O GLN B 755 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 759 " --> pdb=" O TYR B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 759' Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.854A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.509A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.814A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.652A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.679A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.547A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.941A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.567A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.668A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.985A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.080A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.339A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.013A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 7.324A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.568A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 3.914A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.607A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.579A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.532A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.506A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.030A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.562A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.653A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.797A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.481A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.604A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.539A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.519A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.244A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.060A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.819A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.849A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.060A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 722 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 5.805A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.292A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.076A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.592A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.837A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 327 removed outlier: 5.807A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.861A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.222A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 6.527A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.618A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.963A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.882A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.681A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.319A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.830A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 3.927A pdb=" N CYS C 361 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.039A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 719 removed outlier: 6.568A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 719 removed outlier: 6.568A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1123 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 935 hydrogen bonds defined for protein. 2556 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: 4.85 Time building geometry restraints manager: 2.03 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: 6176 1.34 - 1.46: 3511 1.46 - 1.58: 11741 1.58 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 21547 Sorted by residual: bond pdb=" C ASN C 606 " pdb=" N GLN C 607 " ideal model delta sigma weight residual 1.330 1.380 -0.050 1.32e-02 5.74e+03 1.45e+01 bond pdb=" CZ ARG C 34 " pdb=" NH2 ARG C 34 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.02e+01 bond pdb=" CZ ARG A 357 " pdb=" NH2 ARG A 357 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.74e+00 bond pdb=" CZ ARG C 905 " pdb=" NH2 ARG C 905 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.68e+00 bond pdb=" CZ ARG A 328 " pdb=" NH2 ARG A 328 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.63e+00 ... (remaining 21542 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 19503 1.63 - 3.26: 8012 3.26 - 4.90: 1685 4.90 - 6.53: 177 6.53 - 8.16: 16 Bond angle restraints: 29393 Sorted by residual: angle pdb=" CA ASP C 40 " pdb=" CB ASP C 40 " pdb=" CG ASP C 40 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.00e+00 1.00e+00 3.51e+01 angle pdb=" C GLY C1093 " pdb=" N VAL C1094 " pdb=" CA VAL C1094 " ideal model delta sigma weight residual 122.11 128.55 -6.44 1.12e+00 7.97e-01 3.31e+01 angle pdb=" CA PHE C 759 " pdb=" CB PHE C 759 " pdb=" CG PHE C 759 " ideal model delta sigma weight residual 113.80 119.53 -5.73 1.00e+00 1.00e+00 3.28e+01 angle pdb=" CA ASP A 578 " pdb=" CB ASP A 578 " pdb=" CG ASP A 578 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" CA PHE C 275 " pdb=" CB PHE C 275 " pdb=" CG PHE C 275 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 29388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11899 17.77 - 35.54: 726 35.54 - 53.31: 139 53.31 - 71.08: 36 71.08 - 88.85: 20 Dihedral angle restraints: 12820 sinusoidal: 4525 harmonic: 8295 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 165.28 -72.28 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 157.17 -64.17 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -146.21 60.21 1 1.00e+01 1.00e-02 4.83e+01 ... (remaining 12817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2550 0.096 - 0.193: 837 0.193 - 0.289: 81 0.289 - 0.385: 14 0.385 - 0.481: 1 Chirality restraints: 3483 Sorted by residual: chirality pdb=" CA ASP B 571 " pdb=" N ASP B 571 " pdb=" C ASP B 571 " pdb=" CB ASP B 571 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CA ASP C1041 " pdb=" N ASP C1041 " pdb=" C ASP C1041 " pdb=" CB ASP C1041 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA TRP A 104 " pdb=" N TRP A 104 " pdb=" C TRP A 104 " pdb=" CB TRP A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 3480 not shown) Planarity restraints: 3809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " -0.102 2.00e-02 2.50e+03 6.79e-02 1.15e+02 pdb=" CG TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " 0.084 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " 0.048 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.101 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 104 " -0.106 2.00e-02 2.50e+03 6.20e-02 9.61e+01 pdb=" CG TRP B 104 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 104 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP B 104 " 0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP B 104 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP B 104 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 104 " 0.110 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 104 " -0.058 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 104 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP B 104 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 904 " -0.111 2.00e-02 2.50e+03 6.55e-02 8.59e+01 pdb=" CG TYR A 904 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 904 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 904 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 904 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR A 904 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR A 904 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR A 904 " -0.113 2.00e-02 2.50e+03 ... (remaining 3806 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 10860 3.00 - 3.48: 21081 3.48 - 3.95: 33688 3.95 - 4.43: 37433 4.43 - 4.90: 62418 Nonbonded interactions: 165480 Sorted by model distance: nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.530 3.040 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.548 3.040 nonbonded pdb=" OD1 ASP B 294 " pdb=" OG SER B 297 " model vdw 2.549 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.549 3.040 nonbonded pdb=" OD1 ASP A 294 " pdb=" OG SER A 297 " model vdw 2.550 3.040 ... (remaining 165475 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 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 and (name N or name CA or name C or name O or name CB )) or resid 97 throug \ h 112 or (resid 113 and (name N or name CA or name C or name O or name CB )) or \ resid 116 through 124 or (resid 125 and (name N or name CA or name C or name O o \ r name CB )) or resid 126 through 131 or (resid 132 and (name N or name CA or na \ me C or name O or name CB )) or resid 133 or (resid 134 through 138 and (name N \ or name CA or name C or name O or name CB )) or resid 139 through 140 or resid 1 \ 67 through 171 or (resid 172 and (name N or name CA or name C or name O or name \ CB )) or resid 186 through 196 or resid 200 through 211 or (resid 215 and (name \ N or name CA or name C or name O or name CB )) or resid 216 through 217 or (resi \ d 218 and (name N or name CA or name C or name O or name CB )) or resid 219 thro \ ugh 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 238 or (resid 239 and (name N or name CA or name C or name O \ or name CB )) or resid 240 through 308 or (resid 309 and (name N or name CA or \ name C or name O or name CB )) or resid 310 through 332 or (resid 333 through 33 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 335 through \ 345 or (resid 346 through 360 and (name N or name CA or name C or name O or name \ CB )) or resid 361 or (resid 362 through 378 and (name N or name CA or name C o \ r name O or name CB )) or resid 379 or (resid 380 and (name N or name CA or name \ C or name O or name CB )) or resid 381 or (resid 382 through 383 and (name N or \ name CA or name C or name O or name CB )) or resid 384 or (resid 385 through 39 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 391 or (resi \ d 392 through 403 and (name N or name CA or name C or name O or name CB )) or (r \ esid 404 through 411 and (name N or name CA or name C or name O or name CB )) or \ resid 412 through 413 or (resid 414 through 415 and (name N or name CA or name \ C or name O or name CB )) or resid 416 or (resid 417 through 425 and (name N or \ name CA or name C or name O or name CB )) or resid 426 through 427 or (resid 428 \ through 430 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 31 through 432 or (resid 433 through 454 and (name N or name CA or name C or nam \ e O or name CB )) or (resid 462 and (name N or name CA or name C or name O or na \ me CB )) or resid 463 or (resid 464 through 466 and (name N or name CA or name C \ or name O or name CB )) or resid 491 or (resid 492 through 495 and (name N or n \ ame CA or name C or name O or name CB )) or resid 496 or (resid 497 through 498 \ and (name N or name CA or name C or name O or name CB )) or resid 499 or (resid \ 500 through 503 and (name N or name CA or name C or name O or name CB )) or (res \ id 504 through 506 and (name N or name CA or name C or name O or name CB )) or r \ esid 507 or (resid 508 through 515 and (name N or name CA or name C or name O or \ name CB )) or (resid 522 through 524 and (name N or name CA or name C or name O \ or name CB )) or resid 525 through 528 or (resid 529 and (name N or name CA or \ name C or name O or name CB )) or resid 530 through 553 or (resid 554 and (name \ N or name CA or name C or name O or name CB )) or resid 555 through 793 or (resi \ d 794 and (name N or name CA or name C or name O or name CB )) or resid 795 or ( \ resid 796 and (name N or name CA or name C or name O or name CB )) or resid 797 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name C \ B )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 167 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 442 or resid 448 through 501 or resid 503 through 567 or (resid \ 568 and (name N or name CA or name C or name O or name CB )) or resid 569 throug \ h 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or \ resid 572 through 581 or (resid 582 through 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 585 or (resid 586 and (name N or n \ ame CA or name C or name O or name CB )) or resid 587 through 613 or (resid 614 \ and (name N or name CA or name C or name O or name CB )) or resid 615 through 61 \ 8 or (resid 619 and (name N or name CA or name C or name O or name CB )) or resi \ d 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name CA \ or name C or name O or name CB )) or resid 746 through 827 or resid 855 through \ 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) or re \ sid 922 through 1072 or (resid 1073 and (name N or name CA or name C or name O o \ r name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA or \ name C or name O or name CB )) or resid 1119 through 1143 or (resid 1144 throug \ h 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147)) selection = (chain 'C' and (resid 27 through 66 or resid 82 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 110 or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or resid 116 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 through 140 o \ r resid 167 through 187 or (resid 188 and (name N or name CA or name C or name O \ or name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB )) or resid 200 through 241 or (resid 242 through 26 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 265 through \ 280 or (resid 281 and (name N or name CA or name C or name O or name CB )) or re \ sid 282 through 442 or resid 448 through 501 or resid 503 through 567 or (resid \ 568 and (name N or name CA or name C or name O or name CB )) or resid 569 throug \ h 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or \ resid 572 through 581 or (resid 582 through 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 585 or (resid 586 and (name N or n \ ame CA or name C or name O or name CB )) or resid 587 through 613 or (resid 614 \ and (name N or name CA or name C or name O or name CB )) or resid 615 through 61 \ 8 or (resid 619 and (name N or name CA or name C or name O or name CB )) or resi \ d 620 through 676 or resid 690 through 744 or (resid 745 and (name N or name CA \ or name C or name O or name CB )) or resid 746 through 827 or resid 855 through \ 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) or re \ sid 922 through 1072 or (resid 1073 and (name N or name CA or name C or name O o \ r name CB )) or resid 1074 through 1117 or (resid 1118 and (name N or name CA or \ name C or name O or name CB )) or resid 1119 through 1143 or (resid 1144 throug \ h 1146 and (name N or name CA or name C or name O or name CB )) or resid 1147)) } 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.410 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.012 0.050 21581 Z= 0.686 Angle : 1.744 8.160 29461 Z= 1.174 Chirality : 0.088 0.481 3483 Planarity : 0.013 0.147 3809 Dihedral : 13.172 88.847 7342 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.69 % Favored : 92.88 % Rotamer: Outliers : 2.08 % Allowed : 4.71 % Favored : 93.21 % Cbeta Deviations : 0.07 % 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: -1.71 (0.14), residues: 2779 helix: -0.92 (0.17), residues: 649 sheet: -0.41 (0.23), residues: 450 loop : -1.46 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG A 44 TYR 0.113 0.020 TYR A 904 PHE 0.087 0.013 PHE C1121 TRP 0.111 0.023 TRP A 886 HIS 0.018 0.004 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01178 (21547) covalent geometry : angle 1.74424 (29393) SS BOND : bond 0.00714 ( 34) SS BOND : angle 1.56562 ( 68) hydrogen bonds : bond 0.15553 ( 926) hydrogen bonds : angle 9.07420 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6463 (pp) REVERT: A 216 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7997 (pt) outliers start: 45 outliers final: 14 residues processed: 126 average time/residue: 0.1281 time to fit residues: 26.6169 Evaluate side-chains 58 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.0870 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 751 ASN A 777 ASN A 913 GLN A 955 ASN A 957 GLN A1023 ASN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 751 ASN B 777 ASN C 777 ASN C 953 ASN C 955 ASN C 960 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.064522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.045379 restraints weight = 94596.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047096 restraints weight = 42479.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048218 restraints weight = 25365.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048963 restraints weight = 17882.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049387 restraints weight = 14144.044| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21581 Z= 0.136 Angle : 0.606 13.807 29461 Z= 0.324 Chirality : 0.044 0.164 3483 Planarity : 0.004 0.046 3809 Dihedral : 6.392 59.220 3018 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 1.89 % Allowed : 6.00 % Favored : 92.11 % 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: -0.61 (0.15), residues: 2779 helix: 0.98 (0.20), residues: 682 sheet: -0.54 (0.20), residues: 607 loop : -0.99 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 765 TYR 0.015 0.001 TYR A1067 PHE 0.022 0.001 PHE A 497 TRP 0.020 0.002 TRP B 104 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00288 (21547) covalent geometry : angle 0.60056 (29393) SS BOND : bond 0.00648 ( 34) SS BOND : angle 1.85613 ( 68) hydrogen bonds : bond 0.04353 ( 926) hydrogen bonds : angle 6.26980 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 55 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8196 (mmp80) REVERT: A 537 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8947 (mtpt) REVERT: A 740 MET cc_start: 0.8604 (tpt) cc_final: 0.8164 (tpp) REVERT: A 900 MET cc_start: 0.8475 (ttm) cc_final: 0.8135 (mtt) REVERT: B 231 ILE cc_start: 0.8802 (mp) cc_final: 0.8464 (mm) REVERT: B 586 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8535 (t0) REVERT: B 740 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8692 (mtm) REVERT: B 776 LYS cc_start: 0.9461 (tttt) cc_final: 0.9196 (tptt) REVERT: C 584 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8350 (pp) outliers start: 41 outliers final: 20 residues processed: 90 average time/residue: 0.1271 time to fit residues: 19.6223 Evaluate side-chains 68 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 43 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 268 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 224 optimal weight: 50.0000 chunk 62 optimal weight: 3.9990 chunk 273 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 203 optimal weight: 0.2980 chunk 258 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A1048 HIS B 926 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.064414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.045197 restraints weight = 95357.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046899 restraints weight = 43112.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.048029 restraints weight = 25819.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048758 restraints weight = 18212.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049253 restraints weight = 14445.749| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21581 Z= 0.121 Angle : 0.532 11.517 29461 Z= 0.279 Chirality : 0.043 0.151 3483 Planarity : 0.003 0.037 3809 Dihedral : 5.349 57.002 3010 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.08 % Allowed : 6.37 % Favored : 91.55 % 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: -0.16 (0.16), residues: 2779 helix: 1.67 (0.21), residues: 660 sheet: -0.37 (0.20), residues: 645 loop : -0.79 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.017 0.001 TYR A1067 PHE 0.014 0.001 PHE B1121 TRP 0.028 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00260 (21547) covalent geometry : angle 0.52479 (29393) SS BOND : bond 0.00624 ( 34) SS BOND : angle 1.87046 ( 68) hydrogen bonds : bond 0.03652 ( 926) hydrogen bonds : angle 5.67706 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 49 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 514 SER cc_start: 0.9405 (t) cc_final: 0.9133 (p) REVERT: A 900 MET cc_start: 0.8432 (ttm) cc_final: 0.8059 (mtt) REVERT: B 231 ILE cc_start: 0.8954 (mp) cc_final: 0.8680 (mm) REVERT: B 560 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8975 (mm) REVERT: B 584 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8745 (tp) REVERT: B 776 LYS cc_start: 0.9440 (tttt) cc_final: 0.9221 (tptt) REVERT: C 584 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8337 (pp) REVERT: C 731 MET cc_start: 0.8244 (ttm) cc_final: 0.7888 (ttm) outliers start: 45 outliers final: 23 residues processed: 89 average time/residue: 0.1205 time to fit residues: 18.5497 Evaluate side-chains 67 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 41 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 254 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 chunk 55 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A1002 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.065165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046246 restraints weight = 95833.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047960 restraints weight = 43580.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049087 restraints weight = 26135.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049840 restraints weight = 18411.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.050310 restraints weight = 14571.395| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21581 Z= 0.117 Angle : 0.501 14.784 29461 Z= 0.261 Chirality : 0.042 0.144 3483 Planarity : 0.003 0.041 3809 Dihedral : 4.992 58.074 3009 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 2.31 % Allowed : 7.25 % Favored : 90.44 % 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: 0.02 (0.16), residues: 2779 helix: 1.97 (0.21), residues: 648 sheet: -0.44 (0.19), residues: 709 loop : -0.63 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 983 TYR 0.018 0.001 TYR A1067 PHE 0.014 0.001 PHE B1121 TRP 0.015 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00258 (21547) covalent geometry : angle 0.49679 (29393) SS BOND : bond 0.00267 ( 34) SS BOND : angle 1.49454 ( 68) hydrogen bonds : bond 0.03393 ( 926) hydrogen bonds : angle 5.37723 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 49 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 514 SER cc_start: 0.9429 (t) cc_final: 0.9193 (p) REVERT: A 537 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8959 (mtpt) REVERT: A 900 MET cc_start: 0.8285 (ttm) cc_final: 0.7974 (mtt) REVERT: B 560 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8912 (mm) REVERT: C 342 PHE cc_start: 0.7856 (m-80) cc_final: 0.7260 (t80) REVERT: C 584 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8344 (pp) REVERT: C 731 MET cc_start: 0.8138 (ttm) cc_final: 0.7932 (ttm) REVERT: C 1050 MET cc_start: 0.8468 (ptt) cc_final: 0.7994 (ptt) outliers start: 50 outliers final: 29 residues processed: 95 average time/residue: 0.1338 time to fit residues: 21.8611 Evaluate side-chains 70 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 38 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 570 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 226 optimal weight: 40.0000 chunk 89 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 283 optimal weight: 8.9990 chunk 147 optimal weight: 0.0030 chunk 178 optimal weight: 6.9990 chunk 60 optimal weight: 0.3980 overall best weight: 1.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.064703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.045644 restraints weight = 95680.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.047338 restraints weight = 43726.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048444 restraints weight = 26298.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049192 restraints weight = 18659.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.049611 restraints weight = 14794.220| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 21581 Z= 0.139 Angle : 0.505 14.926 29461 Z= 0.260 Chirality : 0.042 0.144 3483 Planarity : 0.003 0.048 3809 Dihedral : 4.827 58.711 3007 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.94 % Allowed : 7.94 % Favored : 90.12 % 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: 0.11 (0.16), residues: 2779 helix: 2.08 (0.21), residues: 643 sheet: -0.42 (0.19), residues: 700 loop : -0.56 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.017 0.001 TYR A1067 PHE 0.024 0.001 PHE A 133 TRP 0.011 0.001 TRP B 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00309 (21547) covalent geometry : angle 0.50024 (29393) SS BOND : bond 0.00230 ( 34) SS BOND : angle 1.57116 ( 68) hydrogen bonds : bond 0.03362 ( 926) hydrogen bonds : angle 5.35098 ( 2556) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 41 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8449 (m-80) cc_final: 0.8012 (m-80) REVERT: A 514 SER cc_start: 0.9418 (t) cc_final: 0.9216 (p) REVERT: A 537 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8957 (mtpt) REVERT: A 900 MET cc_start: 0.8271 (ttm) cc_final: 0.7932 (mtt) REVERT: B 560 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 342 PHE cc_start: 0.7922 (m-80) cc_final: 0.7424 (t80) REVERT: C 584 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8343 (pp) REVERT: C 759 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8190 (t80) REVERT: C 1050 MET cc_start: 0.8630 (ptt) cc_final: 0.8164 (ptt) outliers start: 42 outliers final: 26 residues processed: 79 average time/residue: 0.1015 time to fit residues: 14.5111 Evaluate side-chains 69 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 39 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 856 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 1004 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 31 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 227 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 153 optimal weight: 0.3980 chunk 129 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 0.0060 chunk 38 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 overall best weight: 3.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS B 804 GLN B 935 GLN C 872 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.063524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044704 restraints weight = 94409.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.046283 restraints weight = 44488.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.047311 restraints weight = 27151.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048020 restraints weight = 19473.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.048461 restraints weight = 15507.102| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21581 Z= 0.225 Angle : 0.564 13.864 29461 Z= 0.290 Chirality : 0.043 0.237 3483 Planarity : 0.004 0.049 3809 Dihedral : 5.020 58.827 3007 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 2.35 % Allowed : 8.45 % Favored : 89.20 % 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: 0.01 (0.16), residues: 2779 helix: 2.11 (0.21), residues: 626 sheet: -0.49 (0.19), residues: 704 loop : -0.64 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.018 0.002 TYR A1067 PHE 0.018 0.002 PHE C 92 TRP 0.014 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00496 (21547) covalent geometry : angle 0.56087 (29393) SS BOND : bond 0.00296 ( 34) SS BOND : angle 1.43149 ( 68) hydrogen bonds : bond 0.03633 ( 926) hydrogen bonds : angle 5.54681 ( 2556) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 38 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8454 (ttm) cc_final: 0.8062 (mtt) REVERT: B 560 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8856 (mm) REVERT: B 866 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8415 (p) REVERT: C 342 PHE cc_start: 0.7969 (m-80) cc_final: 0.7463 (t80) REVERT: C 584 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8457 (pp) REVERT: C 697 MET cc_start: 0.8987 (ttm) cc_final: 0.8562 (ttp) REVERT: C 1050 MET cc_start: 0.8839 (ptt) cc_final: 0.8431 (ptt) outliers start: 51 outliers final: 25 residues processed: 84 average time/residue: 0.1137 time to fit residues: 17.0409 Evaluate side-chains 62 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 34 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 260 optimal weight: 0.8980 chunk 132 optimal weight: 0.3980 chunk 265 optimal weight: 0.9990 chunk 221 optimal weight: 50.0000 chunk 173 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.063841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.044789 restraints weight = 95624.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.046436 restraints weight = 44171.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047533 restraints weight = 26733.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.048251 restraints weight = 18969.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048670 restraints weight = 15075.799| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21581 Z= 0.177 Angle : 0.521 14.978 29461 Z= 0.268 Chirality : 0.042 0.198 3483 Planarity : 0.003 0.051 3809 Dihedral : 4.779 57.157 3005 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 1.85 % Allowed : 9.05 % Favored : 89.10 % 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: 0.10 (0.16), residues: 2779 helix: 2.20 (0.21), residues: 626 sheet: -0.46 (0.19), residues: 704 loop : -0.58 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.018 0.001 TYR A1067 PHE 0.015 0.001 PHE B1121 TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00392 (21547) covalent geometry : angle 0.51811 (29393) SS BOND : bond 0.00285 ( 34) SS BOND : angle 1.28481 ( 68) hydrogen bonds : bond 0.03440 ( 926) hydrogen bonds : angle 5.40288 ( 2556) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 39 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8675 (m-80) cc_final: 0.8431 (m-80) REVERT: B 560 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8842 (mm) REVERT: B 1050 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7861 (ptt) REVERT: C 342 PHE cc_start: 0.8008 (m-80) cc_final: 0.7592 (t80) REVERT: C 584 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8356 (pp) REVERT: C 697 MET cc_start: 0.8902 (ttm) cc_final: 0.8467 (ttp) REVERT: C 1050 MET cc_start: 0.8835 (ptt) cc_final: 0.8335 (ptt) outliers start: 40 outliers final: 25 residues processed: 76 average time/residue: 0.1168 time to fit residues: 15.9648 Evaluate side-chains 65 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 37 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 173 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 223 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 200 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 151 optimal weight: 0.0970 chunk 204 optimal weight: 8.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.063697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.044795 restraints weight = 95192.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.046390 restraints weight = 44819.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.047441 restraints weight = 27388.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048144 restraints weight = 19600.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.048585 restraints weight = 15630.275| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21581 Z= 0.183 Angle : 0.532 14.182 29461 Z= 0.273 Chirality : 0.042 0.182 3483 Planarity : 0.003 0.054 3809 Dihedral : 4.749 56.652 3005 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 1.99 % Allowed : 9.19 % Favored : 88.83 % 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: 0.09 (0.16), residues: 2779 helix: 2.16 (0.21), residues: 627 sheet: -0.49 (0.19), residues: 702 loop : -0.56 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.018 0.001 TYR A1067 PHE 0.015 0.001 PHE B1121 TRP 0.013 0.001 TRP A 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00407 (21547) covalent geometry : angle 0.52748 (29393) SS BOND : bond 0.00277 ( 34) SS BOND : angle 1.48033 ( 68) hydrogen bonds : bond 0.03490 ( 926) hydrogen bonds : angle 5.39123 ( 2556) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 40 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.6701 (tp40) REVERT: A 392 PHE cc_start: 0.8666 (m-80) cc_final: 0.8404 (m-80) REVERT: B 560 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8848 (mm) REVERT: B 1050 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7931 (ptt) REVERT: C 342 PHE cc_start: 0.7966 (m-80) cc_final: 0.7561 (t80) REVERT: C 584 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8318 (pp) REVERT: C 697 MET cc_start: 0.8836 (ttm) cc_final: 0.8420 (ttp) REVERT: C 1050 MET cc_start: 0.8845 (ptt) cc_final: 0.8359 (ptt) outliers start: 43 outliers final: 29 residues processed: 79 average time/residue: 0.1178 time to fit residues: 16.7566 Evaluate side-chains 71 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 38 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 148 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 128 optimal weight: 50.0000 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.063588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.044652 restraints weight = 95339.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046239 restraints weight = 44951.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.047304 restraints weight = 27529.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047996 restraints weight = 19676.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048424 restraints weight = 15721.387| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21581 Z= 0.185 Angle : 0.529 13.812 29461 Z= 0.272 Chirality : 0.042 0.189 3483 Planarity : 0.003 0.054 3809 Dihedral : 4.727 56.423 3005 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.39 % Favored : 95.57 % Rotamer: Outliers : 1.89 % Allowed : 9.37 % Favored : 88.73 % 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: 0.10 (0.16), residues: 2779 helix: 2.17 (0.21), residues: 627 sheet: -0.49 (0.19), residues: 700 loop : -0.55 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 765 TYR 0.019 0.001 TYR A1067 PHE 0.015 0.001 PHE B1121 TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00412 (21547) covalent geometry : angle 0.52470 (29393) SS BOND : bond 0.00274 ( 34) SS BOND : angle 1.42179 ( 68) hydrogen bonds : bond 0.03473 ( 926) hydrogen bonds : angle 5.36970 ( 2556) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 36 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 560 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8849 (mm) REVERT: B 1050 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7931 (ptt) REVERT: C 342 PHE cc_start: 0.8000 (m-80) cc_final: 0.7618 (t80) REVERT: C 584 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8315 (pp) REVERT: C 697 MET cc_start: 0.8860 (ttm) cc_final: 0.8431 (ttp) REVERT: C 1050 MET cc_start: 0.8851 (ptt) cc_final: 0.8324 (ptt) outliers start: 41 outliers final: 31 residues processed: 74 average time/residue: 0.1141 time to fit residues: 15.6822 Evaluate side-chains 69 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 35 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 79 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 142 optimal weight: 0.5980 chunk 222 optimal weight: 50.0000 chunk 102 optimal weight: 3.9990 chunk 225 optimal weight: 0.0050 chunk 118 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045532 restraints weight = 96289.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.047222 restraints weight = 44030.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.048328 restraints weight = 26461.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049050 restraints weight = 18732.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.049511 restraints weight = 14861.690| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21581 Z= 0.113 Angle : 0.489 13.356 29461 Z= 0.252 Chirality : 0.042 0.179 3483 Planarity : 0.003 0.058 3809 Dihedral : 4.508 55.597 3005 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.62 % Allowed : 9.56 % Favored : 88.83 % 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: 0.28 (0.16), residues: 2779 helix: 2.22 (0.21), residues: 638 sheet: -0.40 (0.20), residues: 664 loop : -0.40 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.016 0.001 TYR A1067 PHE 0.015 0.001 PHE B1121 TRP 0.014 0.001 TRP B 104 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00250 (21547) covalent geometry : angle 0.48574 (29393) SS BOND : bond 0.00200 ( 34) SS BOND : angle 1.25341 ( 68) hydrogen bonds : bond 0.03247 ( 926) hydrogen bonds : angle 5.18762 ( 2556) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 40 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: A 58 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.7977 (m-10) REVERT: A 239 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7210 (tp40) REVERT: A 392 PHE cc_start: 0.8577 (m-80) cc_final: 0.8328 (m-80) REVERT: A 759 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8295 (t80) REVERT: B 560 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 582 LEU cc_start: 0.9539 (mp) cc_final: 0.9295 (mt) REVERT: B 1050 MET cc_start: 0.8204 (ptm) cc_final: 0.7708 (ptt) REVERT: C 342 PHE cc_start: 0.8031 (m-80) cc_final: 0.6948 (t80) REVERT: C 584 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8268 (pp) REVERT: C 740 MET cc_start: 0.8647 (ppp) cc_final: 0.8361 (pmm) REVERT: C 1050 MET cc_start: 0.8841 (ptt) cc_final: 0.8305 (ptt) outliers start: 35 outliers final: 26 residues processed: 72 average time/residue: 0.1210 time to fit residues: 15.4653 Evaluate side-chains 68 residues out of total 2512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 37 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 69 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 235 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 233 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 213 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.045514 restraints weight = 96404.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047186 restraints weight = 44090.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.048297 restraints weight = 26605.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049026 restraints weight = 18820.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049445 restraints weight = 14938.791| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 21581 Z= 0.170 Angle : 0.693 59.053 29461 Z= 0.388 Chirality : 0.042 0.390 3483 Planarity : 0.003 0.058 3809 Dihedral : 4.506 55.583 3005 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.67 % Favored : 96.29 % Rotamer: Outliers : 1.48 % Allowed : 9.79 % Favored : 88.73 % Cbeta Deviations : 0.04 % 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: 0.28 (0.16), residues: 2779 helix: 2.22 (0.21), residues: 638 sheet: -0.39 (0.20), residues: 664 loop : -0.40 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 765 TYR 0.016 0.001 TYR A1067 PHE 0.015 0.001 PHE B1121 TRP 0.014 0.001 TRP B 104 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00327 (21547) covalent geometry : angle 0.69124 (29393) SS BOND : bond 0.00214 ( 34) SS BOND : angle 1.21322 ( 68) hydrogen bonds : bond 0.03248 ( 926) hydrogen bonds : angle 5.18566 ( 2556) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3341.26 seconds wall clock time: 58 minutes 32.02 seconds (3512.02 seconds total)