Starting phenix.real_space_refine on Thu Mar 5 16:37:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lyn_23596/03_2026/7lyn_23596.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lyn_23596/03_2026/7lyn_23596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lyn_23596/03_2026/7lyn_23596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lyn_23596/03_2026/7lyn_23596.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lyn_23596/03_2026/7lyn_23596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lyn_23596/03_2026/7lyn_23596.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.072 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 103 5.16 5 C 15097 2.51 5 N 3887 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23641 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7713 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7712 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7684 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 5.99, per 1000 atoms: 0.25 Number of scatterers: 23641 At special positions: 0 Unit cell: (130.418, 133.625, 193.489, 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 103 16.00 O 4554 8.00 N 3887 7.00 C 15097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, 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=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B 801 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 801 " Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.1 seconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 46 sheets defined 27.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.818A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.980A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.696A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.947A 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 616 through 620 removed outlier: 3.685A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.034A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.061A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.989A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.661A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.852A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.536A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.682A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.979A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (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 138 through 142 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.108A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.814A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.015A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.892A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.576A 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 912 through 918 removed outlier: 4.121A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (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 965 removed outlier: 3.669A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.569A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.321A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.085A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.930A 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 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.614A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.595A 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: 3.615A 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 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.659A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (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 965 removed outlier: 3.755A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.899A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.348A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.594A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.787A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.818A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.488A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.873A 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 358 removed outlier: 3.961A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.959A 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 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.622A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.398A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.352A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.279A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.769A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.872A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.295A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.149A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.617A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.770A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.995A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.987A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.778A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.307A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.649A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.631A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.555A 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 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.800A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.600A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.915A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.364A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.286A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1098 removed outlier: 3.886A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2805 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: 7.06 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6190 1.33 - 1.45: 4512 1.45 - 1.58: 13331 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24160 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.43e+01 bond pdb=" C5 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG C1313 " pdb=" O5 NAG C1313 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 24155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 25048 2.06 - 4.11: 7245 4.11 - 6.17: 555 6.17 - 8.22: 37 8.22 - 10.28: 3 Bond angle restraints: 32888 Sorted by residual: angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 119.54 -5.74 1.00e+00 1.00e+00 3.29e+01 angle pdb=" CB HIS C1064 " pdb=" CG HIS C1064 " pdb=" CD2 HIS C1064 " ideal model delta sigma weight residual 131.20 123.94 7.26 1.30e+00 5.92e-01 3.12e+01 angle pdb=" CA PHE B 106 " pdb=" CB PHE B 106 " pdb=" CG PHE B 106 " ideal model delta sigma weight residual 113.80 119.23 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.22 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" CA PHE B 515 " pdb=" CB PHE B 515 " pdb=" CG PHE B 515 " ideal model delta sigma weight residual 113.80 119.19 -5.39 1.00e+00 1.00e+00 2.91e+01 ... (remaining 32883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13829 17.82 - 35.64: 795 35.64 - 53.46: 148 53.46 - 71.28: 47 71.28 - 89.11: 22 Dihedral angle restraints: 14841 sinusoidal: 6168 harmonic: 8673 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 -178.30 -88.70 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.98 78.98 1 1.00e+01 1.00e-02 7.77e+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 -154.58 68.58 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 14838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 3864 0.271 - 0.543: 23 0.543 - 0.814: 0 0.814 - 1.085: 0 1.085 - 1.356: 1 Chirality restraints: 3888 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-01 2.50e+01 4.60e+01 chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA ARG B1107 " pdb=" N ARG B1107 " pdb=" C ARG B1107 " pdb=" CB ARG B1107 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 3885 not shown) Planarity restraints: 4229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " 0.230 2.00e-02 2.50e+03 1.30e-01 3.39e+02 pdb=" CG TYR C 904 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " -0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " -0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " -0.088 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.205 2.00e-02 2.50e+03 1.08e-01 2.94e+02 pdb=" CG TRP C 886 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.158 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.120 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " -0.138 2.00e-02 2.50e+03 1.46e-01 2.66e+02 pdb=" CG ASN A 657 " 0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " -0.173 2.00e-02 2.50e+03 ... (remaining 4226 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 11206 2.98 - 3.46: 22483 3.46 - 3.94: 39045 3.94 - 4.42: 43175 4.42 - 4.90: 74093 Nonbonded interactions: 190002 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.504 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.529 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.539 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.540 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.550 3.040 ... (remaining 189997 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 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name 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 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 through 217 or (resid 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 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 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 9 through 810 or (resid 811 and (name N or name CA or name C or name O or name C \ B )) or resid 812 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 1 \ 141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or r \ esid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 through 1312)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 130 or (resid 131 through 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 through 134 or (resid 1 \ 35 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (nam \ e N or name CA or name C or name O or name CB )) or resid 192 through 195 or (re \ sid 196 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 241 or (resid 242 through 264 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 n \ ame CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 \ and (name N or name CA or name C or name O or name CB )) or resid 569 through 58 \ 2 or (resid 583 and (name N or name CA or name C or name O or name CB )) or resi \ d 584 through 585 or (resid 586 and (name N or name CA or name C or name O or na \ me CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name C \ or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or (r \ esid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 t \ hrough 747 or (resid 748 and (name N or name CA or name C or name O or name CB ) \ ) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or nam \ e O or name CB )) or resid 812 through 813 or (resid 814 and (name N or name CA \ or name C or name O or name CB )) or resid 815 through 827 or resid 855 through \ 866 or (resid 867 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 1091 or (resid 1092 and (name N or name CA or name C \ or name O or name CB )) or resid 1093 through 1143 or (resid 1144 through 1146 \ and (name N or name CA or name C or name O or name CB )) or resid 1147 through 1 \ 312)) selection = (chain 'C' 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 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 130 or (resid 131 through 132 and (name N or name CA or name C o \ r name O or name CB )) or resid 133 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 143 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 195 or (resid 196 through 197 and (name N or name CA or name C or name O \ or name CB )) or resid 198 through 213 or (resid 214 and (name N or name CA or \ name C or name O or name CB )) or resid 215 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 238 or (resi \ d 239 and (name N or name CA or name C or name O or name CB )) or resid 240 thro \ ugh 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) o \ r resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O \ or name CB )) or resid 529 through 567 or (resid 568 and (name N or name CA or \ name C or name O or name CB )) or resid 569 through 582 or (resid 583 and (name \ N or name CA or name C or name O or name CB )) or resid 584 through 585 or (resi \ d 586 and (name N or name CA or name C or name O or name CB )) or resid 587 thro \ ugh 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) o \ r resid 620 through 813 or (resid 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 1091 or (resid 1092 and (name N or name CA o \ r name C or name O or name CB )) or resid 1093 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 or (resid 1144 \ through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 through 1312)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.150 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.013 0.076 24236 Z= 0.763 Angle : 1.765 11.511 33078 Z= 1.174 Chirality : 0.096 1.356 3888 Planarity : 0.013 0.192 4191 Dihedral : 12.751 89.105 9147 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.75 % Favored : 93.97 % Rotamer: Outliers : 0.86 % Allowed : 2.39 % Favored : 96.75 % 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: -0.95 (0.14), residues: 2937 helix: -1.01 (0.17), residues: 694 sheet: 0.33 (0.22), residues: 499 loop : -0.72 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1019 TYR 0.230 0.019 TYR C 904 PHE 0.077 0.011 PHE A 718 TRP 0.205 0.026 TRP C 886 HIS 0.009 0.003 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.01328 (24160) covalent geometry : angle 1.74572 (32888) SS BOND : bond 0.01324 ( 38) SS BOND : angle 1.99041 ( 76) hydrogen bonds : bond 0.15874 ( 1029) hydrogen bonds : angle 8.54425 ( 2805) link_NAG-ASN : bond 0.01264 ( 38) link_NAG-ASN : angle 4.65524 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 364 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8587 (mt) cc_final: 0.8310 (mp) REVERT: A 205 SER cc_start: 0.8975 (p) cc_final: 0.8262 (m) REVERT: A 220 PHE cc_start: 0.7155 (t80) cc_final: 0.6772 (t80) REVERT: A 356 LYS cc_start: 0.7852 (tptt) cc_final: 0.7404 (mttt) REVERT: A 429 PHE cc_start: 0.8692 (t80) cc_final: 0.8432 (t80) REVERT: A 590 CYS cc_start: 0.5625 (m) cc_final: 0.5070 (m) REVERT: A 816 SER cc_start: 0.9339 (p) cc_final: 0.8919 (t) REVERT: A 986 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7889 (mmtt) REVERT: B 54 LEU cc_start: 0.8552 (mt) cc_final: 0.8250 (mp) REVERT: B 747 THR cc_start: 0.8415 (m) cc_final: 0.8028 (p) REVERT: B 751 ASN cc_start: 0.8365 (m-40) cc_final: 0.8101 (m110) REVERT: B 776 LYS cc_start: 0.8492 (tttt) cc_final: 0.8177 (ttmt) REVERT: B 854 LYS cc_start: 0.4476 (tttt) cc_final: 0.3987 (ptmt) REVERT: C 237 ARG cc_start: 0.8260 (mtm180) cc_final: 0.7940 (ttp-110) REVERT: C 493 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6873 (mp10) REVERT: C 564 GLN cc_start: 0.7505 (tp40) cc_final: 0.7078 (tp40) REVERT: C 565 PHE cc_start: 0.7714 (p90) cc_final: 0.7425 (p90) REVERT: C 814 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7403 (mttp) REVERT: C 904 TYR cc_start: 0.7911 (m-80) cc_final: 0.7558 (m-10) REVERT: C 984 LEU cc_start: 0.8401 (mt) cc_final: 0.8191 (mp) REVERT: C 990 GLU cc_start: 0.7698 (tt0) cc_final: 0.7358 (mt-10) outliers start: 22 outliers final: 6 residues processed: 383 average time/residue: 0.1854 time to fit residues: 108.2552 Evaluate side-chains 193 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 207 HIS A 354 ASN A 394 ASN A1088 HIS B 414 GLN B 955 ASN C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117288 restraints weight = 33870.209| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.84 r_work: 0.3056 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 24236 Z= 0.143 Angle : 0.650 11.610 33078 Z= 0.336 Chirality : 0.046 0.216 3888 Planarity : 0.004 0.050 4191 Dihedral : 7.190 59.696 3994 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.51 % Rotamer: Outliers : 1.10 % Allowed : 6.66 % Favored : 92.24 % 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 (0.15), residues: 2937 helix: 1.32 (0.20), residues: 659 sheet: 0.23 (0.19), residues: 667 loop : -0.49 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.023 0.002 TYR C 170 PHE 0.023 0.002 PHE C 133 TRP 0.020 0.002 TRP B 64 HIS 0.008 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00326 (24160) covalent geometry : angle 0.61226 (32888) SS BOND : bond 0.00547 ( 38) SS BOND : angle 2.40204 ( 76) hydrogen bonds : bond 0.04427 ( 1029) hydrogen bonds : angle 6.28189 ( 2805) link_NAG-ASN : bond 0.00322 ( 38) link_NAG-ASN : angle 3.26720 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.7704 (m-80) cc_final: 0.7451 (m-80) REVERT: A 205 SER cc_start: 0.9238 (p) cc_final: 0.8916 (m) REVERT: A 220 PHE cc_start: 0.7227 (t80) cc_final: 0.6830 (t80) REVERT: A 356 LYS cc_start: 0.8253 (tptt) cc_final: 0.7928 (mttt) REVERT: A 453 TYR cc_start: 0.8175 (p90) cc_final: 0.7936 (p90) REVERT: A 458 LYS cc_start: 0.8122 (mmtt) cc_final: 0.7246 (mtpt) REVERT: A 986 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7942 (mmtt) REVERT: B 54 LEU cc_start: 0.8591 (mt) cc_final: 0.8377 (mp) REVERT: B 284 THR cc_start: 0.8706 (m) cc_final: 0.8359 (p) REVERT: B 324 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: B 796 ASP cc_start: 0.8035 (t0) cc_final: 0.7791 (t0) REVERT: B 854 LYS cc_start: 0.5341 (tttt) cc_final: 0.4631 (ptmm) REVERT: B 902 MET cc_start: 0.8448 (mmm) cc_final: 0.8225 (tpt) REVERT: C 102 ARG cc_start: 0.6676 (mtt180) cc_final: 0.6421 (mtm180) REVERT: C 237 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8316 (ttp-110) REVERT: C 436 TRP cc_start: 0.8122 (p90) cc_final: 0.7506 (p90) REVERT: C 449 TYR cc_start: 0.7457 (m-80) cc_final: 0.7187 (m-80) REVERT: C 455 LEU cc_start: 0.8715 (tp) cc_final: 0.8407 (mt) REVERT: C 493 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7195 (mp10) REVERT: C 565 PHE cc_start: 0.8259 (p90) cc_final: 0.8026 (p90) REVERT: C 990 GLU cc_start: 0.8311 (tt0) cc_final: 0.8027 (mt-10) REVERT: C 1029 MET cc_start: 0.9077 (tpp) cc_final: 0.8867 (tpp) outliers start: 28 outliers final: 15 residues processed: 248 average time/residue: 0.1687 time to fit residues: 66.7014 Evaluate side-chains 172 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 119 optimal weight: 0.7980 chunk 295 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 197 optimal weight: 0.0570 chunk 78 optimal weight: 0.7980 chunk 156 optimal weight: 0.0670 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 165 ASN A 207 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1083 HIS B1048 HIS C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1048 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.154790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112446 restraints weight = 33767.540| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.98 r_work: 0.2971 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24236 Z= 0.107 Angle : 0.552 9.627 33078 Z= 0.285 Chirality : 0.044 0.195 3888 Planarity : 0.003 0.041 4191 Dihedral : 6.642 57.326 3989 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.69 % Favored : 97.24 % Rotamer: Outliers : 0.86 % Allowed : 8.74 % Favored : 90.40 % 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: 0.52 (0.15), residues: 2937 helix: 2.05 (0.21), residues: 645 sheet: 0.39 (0.19), residues: 666 loop : -0.35 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 214 TYR 0.021 0.001 TYR A1067 PHE 0.016 0.001 PHE A 429 TRP 0.015 0.001 TRP B 64 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00230 (24160) covalent geometry : angle 0.52818 (32888) SS BOND : bond 0.00299 ( 38) SS BOND : angle 1.39007 ( 76) hydrogen bonds : bond 0.03807 ( 1029) hydrogen bonds : angle 5.83139 ( 2805) link_NAG-ASN : bond 0.00276 ( 38) link_NAG-ASN : angle 2.57366 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 SER cc_start: 0.9179 (p) cc_final: 0.8844 (m) REVERT: A 356 LYS cc_start: 0.8264 (tptt) cc_final: 0.8017 (mttt) REVERT: A 458 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7141 (mtpt) REVERT: A 565 PHE cc_start: 0.7565 (p90) cc_final: 0.7197 (p90) REVERT: B 223 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8892 (mp) REVERT: B 854 LYS cc_start: 0.5232 (tttt) cc_final: 0.4586 (ptmt) REVERT: C 237 ARG cc_start: 0.8682 (mtm180) cc_final: 0.8366 (ttp-110) REVERT: C 449 TYR cc_start: 0.7141 (m-80) cc_final: 0.6791 (m-80) REVERT: C 455 LEU cc_start: 0.8654 (tp) cc_final: 0.8148 (mt) REVERT: C 465 GLU cc_start: 0.7574 (tp30) cc_final: 0.7306 (tp30) REVERT: C 565 PHE cc_start: 0.8152 (p90) cc_final: 0.7919 (p90) REVERT: C 990 GLU cc_start: 0.8158 (tt0) cc_final: 0.7881 (mt-10) outliers start: 22 outliers final: 11 residues processed: 215 average time/residue: 0.1687 time to fit residues: 58.7040 Evaluate side-chains 170 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 127 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 165 optimal weight: 0.0030 chunk 250 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 overall best weight: 2.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 165 ASN A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 87 ASN B 901 GLN B 907 ASN B 935 GLN B 965 GLN C 87 ASN C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.150459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108001 restraints weight = 33860.961| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.96 r_work: 0.2899 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 24236 Z= 0.250 Angle : 0.621 8.591 33078 Z= 0.319 Chirality : 0.047 0.194 3888 Planarity : 0.004 0.040 4191 Dihedral : 6.715 58.704 3987 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 1.80 % Allowed : 9.60 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 2937 helix: 1.64 (0.21), residues: 652 sheet: 0.31 (0.19), residues: 664 loop : -0.50 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 190 TYR 0.023 0.002 TYR A 453 PHE 0.028 0.002 PHE C 140 TRP 0.010 0.001 TRP B 64 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00604 (24160) covalent geometry : angle 0.60063 (32888) SS BOND : bond 0.00475 ( 38) SS BOND : angle 1.59208 ( 76) hydrogen bonds : bond 0.04440 ( 1029) hydrogen bonds : angle 5.96281 ( 2805) link_NAG-ASN : bond 0.00357 ( 38) link_NAG-ASN : angle 2.49266 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.4802 (OUTLIER) cc_final: 0.4384 (m110) REVERT: A 220 PHE cc_start: 0.7482 (t80) cc_final: 0.6845 (t80) REVERT: A 458 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7198 (mtpt) REVERT: A 902 MET cc_start: 0.8785 (tpt) cc_final: 0.8527 (mmt) REVERT: A 985 ASP cc_start: 0.8551 (p0) cc_final: 0.8322 (p0) REVERT: B 269 TYR cc_start: 0.8204 (m-10) cc_final: 0.7960 (m-80) REVERT: B 854 LYS cc_start: 0.5578 (tttt) cc_final: 0.4715 (ptmt) REVERT: C 436 TRP cc_start: 0.8380 (p90) cc_final: 0.7434 (p90) REVERT: C 449 TYR cc_start: 0.7280 (m-80) cc_final: 0.6847 (m-80) REVERT: C 493 GLN cc_start: 0.6923 (mt0) cc_final: 0.6662 (mp10) REVERT: C 564 GLN cc_start: 0.7821 (tp40) cc_final: 0.7485 (tp40) REVERT: C 565 PHE cc_start: 0.8218 (p90) cc_final: 0.7956 (p90) REVERT: C 574 ASP cc_start: 0.8666 (t0) cc_final: 0.8355 (t0) REVERT: C 990 GLU cc_start: 0.8136 (tt0) cc_final: 0.7872 (mt-10) outliers start: 46 outliers final: 33 residues processed: 213 average time/residue: 0.1659 time to fit residues: 56.7177 Evaluate side-chains 181 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 280 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 159 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 804 GLN B 901 GLN C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 762 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.153052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.111295 restraints weight = 33363.482| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.80 r_work: 0.3034 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24236 Z= 0.116 Angle : 0.529 10.818 33078 Z= 0.271 Chirality : 0.044 0.179 3888 Planarity : 0.003 0.037 4191 Dihedral : 6.320 56.836 3987 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Rotamer: Outliers : 1.41 % Allowed : 11.09 % Favored : 87.50 % 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: 0.48 (0.15), residues: 2937 helix: 2.02 (0.21), residues: 645 sheet: 0.37 (0.20), residues: 638 loop : -0.37 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.023 0.001 TYR A 453 PHE 0.031 0.001 PHE C 140 TRP 0.011 0.001 TRP B 64 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00262 (24160) covalent geometry : angle 0.50811 (32888) SS BOND : bond 0.00304 ( 38) SS BOND : angle 1.86423 ( 76) hydrogen bonds : bond 0.03523 ( 1029) hydrogen bonds : angle 5.63626 ( 2805) link_NAG-ASN : bond 0.00228 ( 38) link_NAG-ASN : angle 2.09972 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.5241 (OUTLIER) cc_final: 0.4995 (m-40) REVERT: A 220 PHE cc_start: 0.7549 (t80) cc_final: 0.6857 (t80) REVERT: A 400 PHE cc_start: 0.8438 (p90) cc_final: 0.8114 (p90) REVERT: A 902 MET cc_start: 0.8804 (tpt) cc_final: 0.8461 (mmt) REVERT: A 935 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: A 985 ASP cc_start: 0.8511 (p0) cc_final: 0.8284 (p0) REVERT: B 240 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7563 (t) REVERT: B 347 PHE cc_start: 0.4445 (OUTLIER) cc_final: 0.4023 (t80) REVERT: B 854 LYS cc_start: 0.5611 (tttt) cc_final: 0.4691 (ptmt) REVERT: C 436 TRP cc_start: 0.8381 (p90) cc_final: 0.7459 (p90) REVERT: C 449 TYR cc_start: 0.7553 (m-80) cc_final: 0.7012 (m-80) REVERT: C 564 GLN cc_start: 0.7844 (tp40) cc_final: 0.7527 (tp40) REVERT: C 565 PHE cc_start: 0.8178 (p90) cc_final: 0.7902 (p90) REVERT: C 916 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8910 (tp) REVERT: C 990 GLU cc_start: 0.8203 (tt0) cc_final: 0.7943 (mt-10) outliers start: 36 outliers final: 18 residues processed: 194 average time/residue: 0.1508 time to fit residues: 48.4948 Evaluate side-chains 171 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 187 optimal weight: 0.0020 chunk 102 optimal weight: 0.3980 chunk 229 optimal weight: 10.0000 chunk 213 optimal weight: 0.0470 chunk 89 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.4486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 901 GLN C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.154795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.112782 restraints weight = 33674.960| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.93 r_work: 0.2994 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24236 Z= 0.094 Angle : 0.497 8.587 33078 Z= 0.254 Chirality : 0.043 0.184 3888 Planarity : 0.003 0.041 4191 Dihedral : 6.013 55.225 3987 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 1.61 % Allowed : 11.36 % Favored : 87.03 % 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: 0.66 (0.15), residues: 2937 helix: 2.31 (0.21), residues: 652 sheet: 0.42 (0.19), residues: 646 loop : -0.30 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.022 0.001 TYR A 453 PHE 0.032 0.001 PHE C 140 TRP 0.010 0.001 TRP B 64 HIS 0.005 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00205 (24160) covalent geometry : angle 0.48127 (32888) SS BOND : bond 0.00286 ( 38) SS BOND : angle 1.45465 ( 76) hydrogen bonds : bond 0.03204 ( 1029) hydrogen bonds : angle 5.39190 ( 2805) link_NAG-ASN : bond 0.00208 ( 38) link_NAG-ASN : angle 1.86285 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 VAL cc_start: 0.9057 (t) cc_final: 0.8849 (p) REVERT: A 220 PHE cc_start: 0.7583 (t80) cc_final: 0.6844 (t80) REVERT: A 565 PHE cc_start: 0.7585 (p90) cc_final: 0.7298 (p90) REVERT: A 902 MET cc_start: 0.8760 (tpt) cc_final: 0.8375 (mmp) REVERT: A 935 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7712 (mt0) REVERT: B 854 LYS cc_start: 0.5570 (tttt) cc_final: 0.4787 (ptmt) REVERT: C 326 ILE cc_start: 0.8693 (mt) cc_final: 0.8413 (mm) REVERT: C 436 TRP cc_start: 0.8343 (p90) cc_final: 0.7697 (p90) REVERT: C 449 TYR cc_start: 0.7106 (m-80) cc_final: 0.6678 (m-80) REVERT: C 564 GLN cc_start: 0.7828 (tp40) cc_final: 0.7534 (tp40) REVERT: C 565 PHE cc_start: 0.8037 (p90) cc_final: 0.7472 (p90) REVERT: C 855 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6048 (m-10) REVERT: C 990 GLU cc_start: 0.7956 (tt0) cc_final: 0.7736 (mt-10) outliers start: 41 outliers final: 27 residues processed: 215 average time/residue: 0.1493 time to fit residues: 53.0491 Evaluate side-chains 183 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 253 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 257 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110878 restraints weight = 33563.791| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.93 r_work: 0.2992 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24236 Z= 0.161 Angle : 0.529 6.881 33078 Z= 0.271 Chirality : 0.044 0.186 3888 Planarity : 0.003 0.037 4191 Dihedral : 6.106 56.911 3987 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 1.68 % Allowed : 11.68 % Favored : 86.64 % 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: 0.47 (0.15), residues: 2937 helix: 1.99 (0.21), residues: 661 sheet: 0.37 (0.19), residues: 690 loop : -0.40 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 357 TYR 0.022 0.001 TYR A 453 PHE 0.032 0.001 PHE C 140 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00384 (24160) covalent geometry : angle 0.51462 (32888) SS BOND : bond 0.00388 ( 38) SS BOND : angle 1.34683 ( 76) hydrogen bonds : bond 0.03608 ( 1029) hydrogen bonds : angle 5.52273 ( 2805) link_NAG-ASN : bond 0.00222 ( 38) link_NAG-ASN : angle 1.91741 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7564 (t80) cc_final: 0.6839 (t80) REVERT: A 421 TYR cc_start: 0.7868 (m-80) cc_final: 0.7651 (m-80) REVERT: A 456 PHE cc_start: 0.8045 (m-80) cc_final: 0.7714 (m-80) REVERT: A 565 PHE cc_start: 0.7784 (p90) cc_final: 0.7495 (p90) REVERT: A 902 MET cc_start: 0.8854 (tpt) cc_final: 0.8528 (mmt) REVERT: A 935 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: A 985 ASP cc_start: 0.8546 (p0) cc_final: 0.8301 (p0) REVERT: B 854 LYS cc_start: 0.5695 (tttt) cc_final: 0.4753 (ptmt) REVERT: C 436 TRP cc_start: 0.8429 (p90) cc_final: 0.7582 (p90) REVERT: C 449 TYR cc_start: 0.7660 (m-80) cc_final: 0.7085 (m-80) REVERT: C 564 GLN cc_start: 0.7934 (tp40) cc_final: 0.7630 (tp40) REVERT: C 565 PHE cc_start: 0.8237 (p90) cc_final: 0.7653 (p90) REVERT: C 855 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6240 (m-10) REVERT: C 990 GLU cc_start: 0.8223 (tt0) cc_final: 0.7955 (mt-10) outliers start: 43 outliers final: 34 residues processed: 196 average time/residue: 0.1537 time to fit residues: 50.0098 Evaluate side-chains 188 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 267 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 274 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 128 optimal weight: 0.4980 chunk 229 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.152177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108574 restraints weight = 33619.236| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.07 r_work: 0.2970 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24236 Z= 0.149 Angle : 0.520 7.694 33078 Z= 0.267 Chirality : 0.044 0.183 3888 Planarity : 0.003 0.039 4191 Dihedral : 6.086 57.076 3987 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 1.57 % Allowed : 12.11 % Favored : 86.32 % 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: 0.48 (0.15), residues: 2937 helix: 1.97 (0.21), residues: 661 sheet: 0.34 (0.19), residues: 676 loop : -0.35 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 466 TYR 0.024 0.001 TYR B 200 PHE 0.033 0.001 PHE C 140 TRP 0.017 0.001 TRP A 436 HIS 0.004 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00353 (24160) covalent geometry : angle 0.50609 (32888) SS BOND : bond 0.00347 ( 38) SS BOND : angle 1.23740 ( 76) hydrogen bonds : bond 0.03533 ( 1029) hydrogen bonds : angle 5.48300 ( 2805) link_NAG-ASN : bond 0.00205 ( 38) link_NAG-ASN : angle 1.88273 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7540 (t80) cc_final: 0.6856 (t80) REVERT: A 421 TYR cc_start: 0.7971 (m-80) cc_final: 0.7763 (m-80) REVERT: A 565 PHE cc_start: 0.7789 (p90) cc_final: 0.7518 (p90) REVERT: A 902 MET cc_start: 0.8842 (tpt) cc_final: 0.8496 (mmt) REVERT: A 935 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: A 985 ASP cc_start: 0.8492 (p0) cc_final: 0.8286 (p0) REVERT: B 854 LYS cc_start: 0.5625 (tttt) cc_final: 0.4744 (ptmt) REVERT: C 436 TRP cc_start: 0.8441 (p90) cc_final: 0.7658 (p90) REVERT: C 449 TYR cc_start: 0.7718 (m-80) cc_final: 0.7138 (m-80) REVERT: C 564 GLN cc_start: 0.7963 (tp40) cc_final: 0.7654 (tp40) REVERT: C 565 PHE cc_start: 0.8230 (p90) cc_final: 0.7644 (p90) REVERT: C 855 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6189 (m-10) REVERT: C 990 GLU cc_start: 0.8173 (tt0) cc_final: 0.7914 (mt-10) outliers start: 40 outliers final: 35 residues processed: 188 average time/residue: 0.1483 time to fit residues: 46.2705 Evaluate side-chains 189 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 240 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 231 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 196 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 422 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.149746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106298 restraints weight = 34050.079| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.00 r_work: 0.2938 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24236 Z= 0.264 Angle : 0.599 8.245 33078 Z= 0.307 Chirality : 0.046 0.187 3888 Planarity : 0.004 0.038 4191 Dihedral : 6.396 59.410 3987 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 1.57 % Allowed : 12.34 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 2937 helix: 1.55 (0.21), residues: 667 sheet: 0.20 (0.19), residues: 688 loop : -0.50 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1014 TYR 0.022 0.002 TYR A1067 PHE 0.034 0.002 PHE C 140 TRP 0.012 0.001 TRP A 436 HIS 0.007 0.002 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00638 (24160) covalent geometry : angle 0.58391 (32888) SS BOND : bond 0.00469 ( 38) SS BOND : angle 1.51695 ( 76) hydrogen bonds : bond 0.04170 ( 1029) hydrogen bonds : angle 5.74712 ( 2805) link_NAG-ASN : bond 0.00359 ( 38) link_NAG-ASN : angle 2.06706 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7610 (t80) cc_final: 0.6935 (t80) REVERT: A 421 TYR cc_start: 0.8055 (m-80) cc_final: 0.7840 (m-80) REVERT: A 565 PHE cc_start: 0.7890 (p90) cc_final: 0.7662 (p90) REVERT: A 902 MET cc_start: 0.8865 (tpt) cc_final: 0.8608 (mmt) REVERT: A 985 ASP cc_start: 0.8581 (p0) cc_final: 0.8351 (p0) REVERT: B 854 LYS cc_start: 0.5638 (tttt) cc_final: 0.4715 (ptmt) REVERT: C 409 GLN cc_start: 0.7357 (pt0) cc_final: 0.7071 (pt0) REVERT: C 418 ILE cc_start: 0.8792 (mm) cc_final: 0.8486 (mp) REVERT: C 436 TRP cc_start: 0.8492 (p90) cc_final: 0.7702 (p90) REVERT: C 565 PHE cc_start: 0.8258 (p90) cc_final: 0.7985 (p90) REVERT: C 855 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6284 (m-10) REVERT: C 990 GLU cc_start: 0.8239 (tt0) cc_final: 0.7979 (mt-10) outliers start: 40 outliers final: 35 residues processed: 178 average time/residue: 0.1489 time to fit residues: 44.3571 Evaluate side-chains 184 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 215 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 262 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 321 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109630 restraints weight = 33655.716| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.83 r_work: 0.3000 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24236 Z= 0.145 Angle : 0.526 8.592 33078 Z= 0.270 Chirality : 0.044 0.176 3888 Planarity : 0.003 0.039 4191 Dihedral : 6.179 58.099 3987 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 1.49 % Allowed : 12.58 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.15), residues: 2937 helix: 1.74 (0.21), residues: 674 sheet: 0.27 (0.19), residues: 672 loop : -0.46 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 454 TYR 0.024 0.001 TYR B 365 PHE 0.033 0.001 PHE C 140 TRP 0.015 0.001 TRP C 104 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00344 (24160) covalent geometry : angle 0.51272 (32888) SS BOND : bond 0.00351 ( 38) SS BOND : angle 1.25342 ( 76) hydrogen bonds : bond 0.03549 ( 1029) hydrogen bonds : angle 5.53037 ( 2805) link_NAG-ASN : bond 0.00212 ( 38) link_NAG-ASN : angle 1.87041 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7564 (t80) cc_final: 0.6816 (t80) REVERT: A 565 PHE cc_start: 0.7823 (p90) cc_final: 0.7622 (p90) REVERT: A 902 MET cc_start: 0.8845 (tpt) cc_final: 0.8492 (mmt) REVERT: A 985 ASP cc_start: 0.8477 (p0) cc_final: 0.8260 (p0) REVERT: B 854 LYS cc_start: 0.5514 (tttt) cc_final: 0.4671 (ptmt) REVERT: C 409 GLN cc_start: 0.7378 (pt0) cc_final: 0.7064 (pt0) REVERT: C 436 TRP cc_start: 0.8461 (p90) cc_final: 0.7680 (p90) REVERT: C 452 LEU cc_start: 0.7750 (tp) cc_final: 0.7446 (tp) REVERT: C 565 PHE cc_start: 0.8159 (p90) cc_final: 0.7610 (p90) REVERT: C 855 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6246 (m-10) REVERT: C 990 GLU cc_start: 0.8130 (tt0) cc_final: 0.7886 (mt-10) outliers start: 38 outliers final: 35 residues processed: 179 average time/residue: 0.1452 time to fit residues: 43.6485 Evaluate side-chains 183 residues out of total 2609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 279 optimal weight: 0.0370 chunk 117 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 205 optimal weight: 7.9990 chunk 257 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 135 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107248 restraints weight = 33414.969| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.87 r_work: 0.2968 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24236 Z= 0.199 Angle : 0.557 8.541 33078 Z= 0.285 Chirality : 0.045 0.243 3888 Planarity : 0.003 0.037 4191 Dihedral : 6.248 58.417 3987 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 1.65 % Allowed : 12.62 % Favored : 85.74 % 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: 0.23 (0.15), residues: 2937 helix: 1.65 (0.21), residues: 674 sheet: 0.23 (0.19), residues: 670 loop : -0.51 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 190 TYR 0.034 0.002 TYR C 453 PHE 0.034 0.001 PHE C 140 TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00479 (24160) covalent geometry : angle 0.54275 (32888) SS BOND : bond 0.00403 ( 38) SS BOND : angle 1.37379 ( 76) hydrogen bonds : bond 0.03817 ( 1029) hydrogen bonds : angle 5.59690 ( 2805) link_NAG-ASN : bond 0.00276 ( 38) link_NAG-ASN : angle 1.93185 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6165.16 seconds wall clock time: 106 minutes 19.61 seconds (6379.61 seconds total)