Starting phenix.real_space_refine on Sat Jul 4 08:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lwq_23554/07_2026/7lwq_23554.map" } resolution = 3.44 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12268 2.51 5 N 3171 2.21 5 O 3750 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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19273 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3250 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 1 Chain: "C" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7808 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 chiralities: 12 Time building chain proxies: 3.64, per 1000 atoms: 0.19 Number of scatterers: 19273 At special positions: 0 Unit cell: (127.211, 124.004, 177.454, 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 84 16.00 O 3750 8.00 N 3171 7.00 C 12268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.05 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.01 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A1098 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C1098 " " NAG D 1 " - " ASN B1134 " Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 762.8 milliseconds 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 37 sheets defined 31.3% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 5.232A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.028A 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 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.557A 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: 3.538A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.900A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.555A 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 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.691A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.638A 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.720A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (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 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.754A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 5.468A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.548A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.680A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.733A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 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: 3.755A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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: 3.662A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.379A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.796A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.294A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.581A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.836A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.156A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.453A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.806A 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 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.605A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.540A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.545A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.775A 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 removed outlier: 3.965A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.558A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.396A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.925A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 90 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 192 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.472A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 552 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.746A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.131A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.902A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.398A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.009A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.571A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 567 removed outlier: 4.791A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.741A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.573A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.503A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.254A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.642A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 701 through 703 removed outlier: 5.769A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.680A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.063A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.949A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.532A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.713A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.763A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.640A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.510A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.510A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.605A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2388 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: 3.98 Time building geometry restraints manager: 1.90 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: 4917 1.33 - 1.46: 3773 1.46 - 1.58: 10883 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 19680 Sorted by residual: bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " 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 A1312 " pdb=" O5 NAG A1312 " 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 C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 19675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 23006 2.61 - 5.23: 3639 5.23 - 7.84: 122 7.84 - 10.46: 0 10.46 - 13.07: 1 Bond angle restraints: 26768 Sorted by residual: angle pdb=" CA PHE A 201 " pdb=" CB PHE A 201 " pdb=" CG PHE A 201 " ideal model delta sigma weight residual 113.80 119.33 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CB HIS A1064 " pdb=" CG HIS A1064 " pdb=" CD2 HIS A1064 " ideal model delta sigma weight residual 131.20 124.46 6.74 1.30e+00 5.92e-01 2.69e+01 angle pdb=" OE1 GLN C 965 " pdb=" CD GLN C 965 " pdb=" NE2 GLN C 965 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N LEU A 229 " pdb=" CA LEU A 229 " pdb=" C LEU A 229 " ideal model delta sigma weight residual 110.07 116.51 -6.44 1.26e+00 6.30e-01 2.62e+01 angle pdb=" OE1 GLN B1054 " pdb=" CD GLN B1054 " pdb=" NE2 GLN B1054 " ideal model delta sigma weight residual 122.60 117.51 5.09 1.00e+00 1.00e+00 2.59e+01 ... (remaining 26763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 10657 17.92 - 35.84: 674 35.84 - 53.77: 108 53.77 - 71.69: 33 71.69 - 89.61: 41 Dihedral angle restraints: 11513 sinusoidal: 4468 harmonic: 7045 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 177.38 -84.38 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CA SER A 221 " pdb=" C SER A 221 " pdb=" N ALA A 222 " pdb=" CA ALA A 222 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA PRO C 807 " pdb=" C PRO C 807 " pdb=" N ASP C 808 " pdb=" CA ASP C 808 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 11510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 3138 0.278 - 0.556: 20 0.556 - 0.835: 0 0.835 - 1.113: 0 1.113 - 1.391: 1 Chirality restraints: 3159 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-01 2.50e+01 4.84e+01 chirality pdb=" CA ASP C 745 " pdb=" N ASP C 745 " pdb=" C ASP C 745 " pdb=" CB ASP C 745 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 3156 not shown) Planarity restraints: 3455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 282 " 0.139 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN C 282 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 282 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 282 " -0.230 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.141 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN C 331 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.227 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 204 " 0.211 2.00e-02 2.50e+03 1.15e-01 2.66e+02 pdb=" CG TYR A 204 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 204 " -0.118 2.00e-02 2.50e+03 pdb=" CD2 TYR A 204 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR A 204 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 204 " -0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 204 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 204 " 0.167 2.00e-02 2.50e+03 ... (remaining 3452 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 9722 3.00 - 3.47: 19114 3.47 - 3.95: 31871 3.95 - 4.42: 34877 4.42 - 4.90: 58874 Nonbonded interactions: 154458 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.519 3.040 nonbonded pdb=" OG1 THR A 581 " pdb=" OE1 GLU A 583 " model vdw 2.543 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.549 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.557 3.040 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.564 3.040 ... (remaining 154453 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 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1312)) selection = chain 'C' } 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: 1.660 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.780 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 0.078 19738 Z= 0.766 Angle : 1.788 13.073 26913 Z= 1.185 Chirality : 0.100 1.391 3159 Planarity : 0.014 0.200 3427 Dihedral : 13.843 89.610 6884 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.57 % Favored : 93.05 % Rotamer: Outliers : 1.18 % Allowed : 3.27 % Favored : 95.55 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 2389 helix: -0.82 (0.17), residues: 653 sheet: -0.13 (0.23), residues: 395 loop : -1.14 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 403 TYR 0.211 0.023 TYR A 204 PHE 0.126 0.012 PHE A 86 TRP 0.103 0.025 TRP C 104 HIS 0.009 0.003 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.01327 / 0.77 (19680) covalent geometry : angle 1.77117 / 1.18 (26768) SS BOND : bond 0.01137 / 0.76 ( 29) SS BOND : angle 1.68420 / 1.12 ( 58) hydrogen bonds : bond 0.16966 / 10.89 ( 844) hydrogen bonds : angle 8.52545 / 5.88 ( 2388) link_BETA1-4 : bond 0.03248 / 1.71 ( 1) link_BETA1-4 : angle 5.23264 / 3.41 ( 3) link_NAG-ASN : bond 0.01323 / 0.77 ( 28) link_NAG-ASN : angle 4.66429 / 3.07 ( 84) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 0.517 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: A 223 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5677 (mt) REVERT: A 590 CYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4215 (p) REVERT: B 856 ASN cc_start: 0.7221 (m-40) cc_final: 0.6822 (m-40) REVERT: B 1142 GLN cc_start: 0.9123 (tp40) cc_final: 0.8804 (tp-100) REVERT: C 195 LYS cc_start: 0.6347 (pttt) cc_final: 0.5891 (ptpp) REVERT: C 552 LEU cc_start: 0.9237 (mt) cc_final: 0.8827 (tp) REVERT: C 907 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8723 (t0) REVERT: C 1029 MET cc_start: 0.9255 (tpp) cc_final: 0.8892 (tpp) outliers start: 25 outliers final: 6 residues processed: 280 average time/residue: 0.1312 time to fit residues: 55.7932 Evaluate side-chains 134 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 779 GLN A 960 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 450 ASN C 675 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.137640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098821 restraints weight = 44298.789| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.73 r_work: 0.3342 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 19738 Z= 0.149 Angle : 0.724 11.123 26913 Z= 0.372 Chirality : 0.048 0.383 3159 Planarity : 0.004 0.045 3427 Dihedral : 6.715 59.049 2596 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.99 % Rotamer: Outliers : 1.56 % Allowed : 7.39 % Favored : 91.05 % 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 (0.16), residues: 2389 helix: 1.15 (0.20), residues: 650 sheet: -0.17 (0.21), residues: 479 loop : -0.94 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 646 TYR 0.023 0.002 TYR C 369 PHE 0.041 0.002 PHE C 823 TRP 0.013 0.002 TRP A 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (19680) covalent geometry : angle 0.68223 / 0.36 (26768) SS BOND : bond 0.00378 / 0.26 ( 29) SS BOND : angle 2.15300 / 1.40 ( 58) hydrogen bonds : bond 0.05115 / 3.26 ( 844) hydrogen bonds : angle 6.17138 / 4.24 ( 2388) link_BETA1-4 : bond 0.02108 / 1.11 ( 1) link_BETA1-4 : angle 1.36681 / 0.81 ( 3) link_NAG-ASN : bond 0.00537 / 0.30 ( 28) link_NAG-ASN : angle 4.06351 / 2.66 ( 84) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.7379 (m-30) cc_final: 0.7176 (m-30) REVERT: A 559 PHE cc_start: 0.0274 (OUTLIER) cc_final: -0.1275 (m-80) REVERT: A 590 CYS cc_start: 0.5458 (OUTLIER) cc_final: 0.5081 (p) REVERT: A 779 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7854 (tp-100) REVERT: A 808 ASP cc_start: 0.6354 (t0) cc_final: 0.5956 (p0) REVERT: A 868 GLU cc_start: 0.8473 (tp30) cc_final: 0.8247 (mm-30) REVERT: A 869 MET cc_start: 0.8574 (mtm) cc_final: 0.8333 (mtp) REVERT: A 882 ILE cc_start: 0.9200 (mt) cc_final: 0.8887 (mp) REVERT: A 947 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8455 (mttp) REVERT: B 887 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 1029 MET cc_start: 0.8694 (tpp) cc_final: 0.8442 (tpp) REVERT: C 552 LEU cc_start: 0.9066 (mt) cc_final: 0.8716 (tp) REVERT: C 907 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8974 (t0) REVERT: C 1029 MET cc_start: 0.9313 (tpp) cc_final: 0.8991 (tpp) REVERT: C 1141 LEU cc_start: 0.9519 (tp) cc_final: 0.9282 (mm) outliers start: 33 outliers final: 12 residues processed: 190 average time/residue: 0.1278 time to fit residues: 38.9937 Evaluate side-chains 129 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 53 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 117 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 764 ASN A 779 GLN A 784 GLN A 955 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 644 GLN C 954 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.132915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094774 restraints weight = 45059.246| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.64 r_work: 0.3256 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 19738 Z= 0.279 Angle : 0.746 8.879 26913 Z= 0.383 Chirality : 0.049 0.338 3159 Planarity : 0.004 0.042 3427 Dihedral : 6.257 58.267 2584 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.73 % Favored : 95.23 % Rotamer: Outliers : 2.42 % Allowed : 9.43 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.16), residues: 2389 helix: 1.05 (0.20), residues: 650 sheet: -0.41 (0.21), residues: 448 loop : -1.09 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1019 TYR 0.023 0.002 TYR A 508 PHE 0.027 0.002 PHE A 888 TRP 0.014 0.002 TRP A 436 HIS 0.008 0.002 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.28 (19680) covalent geometry : angle 0.71915 / 0.38 (26768) SS BOND : bond 0.00408 / 0.28 ( 29) SS BOND : angle 1.60351 / 1.02 ( 58) hydrogen bonds : bond 0.05341 / 3.40 ( 844) hydrogen bonds : angle 6.10638 / 4.20 ( 2388) link_BETA1-4 : bond 0.00722 / 0.38 ( 1) link_BETA1-4 : angle 1.89275 / 1.02 ( 3) link_NAG-ASN : bond 0.00490 / 0.32 ( 28) link_NAG-ASN : angle 3.41346 / 2.23 ( 84) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.8558 (t) cc_final: 0.8341 (m) REVERT: A 441 LEU cc_start: 0.8445 (mt) cc_final: 0.8168 (mp) REVERT: A 559 PHE cc_start: 0.1202 (OUTLIER) cc_final: -0.0506 (m-80) REVERT: A 590 CYS cc_start: 0.5554 (OUTLIER) cc_final: 0.5263 (p) REVERT: A 947 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8529 (mtmm) REVERT: A 1138 TYR cc_start: 0.8624 (t80) cc_final: 0.8401 (t80) REVERT: B 762 GLN cc_start: 0.8663 (pt0) cc_final: 0.8419 (pt0) REVERT: B 887 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8592 (p) REVERT: B 990 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6988 (tm-30) REVERT: C 552 LEU cc_start: 0.9206 (mt) cc_final: 0.8847 (tp) REVERT: C 896 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8762 (tt) REVERT: C 907 ASN cc_start: 0.9368 (OUTLIER) cc_final: 0.9051 (t0) REVERT: C 1029 MET cc_start: 0.9291 (tpp) cc_final: 0.9079 (tpp) REVERT: C 1141 LEU cc_start: 0.9388 (tp) cc_final: 0.8861 (pp) outliers start: 51 outliers final: 31 residues processed: 153 average time/residue: 0.1199 time to fit residues: 30.1995 Evaluate side-chains 136 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 151 optimal weight: 30.0000 chunk 211 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.135709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.100248 restraints weight = 43915.834| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.23 r_work: 0.3310 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19738 Z= 0.133 Angle : 0.602 8.383 26913 Z= 0.307 Chirality : 0.045 0.297 3159 Planarity : 0.004 0.038 3427 Dihedral : 5.718 59.638 2584 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.01 % Favored : 96.94 % Rotamer: Outliers : 1.66 % Allowed : 10.52 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2389 helix: 1.62 (0.21), residues: 650 sheet: -0.36 (0.21), residues: 465 loop : -1.00 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE A 400 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (19680) covalent geometry : angle 0.57943 / 0.30 (26768) SS BOND : bond 0.00320 / 0.21 ( 29) SS BOND : angle 1.24427 / 0.75 ( 58) hydrogen bonds : bond 0.04187 / 2.67 ( 844) hydrogen bonds : angle 5.62701 / 3.88 ( 2388) link_BETA1-4 : bond 0.00551 / 0.29 ( 1) link_BETA1-4 : angle 1.34557 / 0.82 ( 3) link_NAG-ASN : bond 0.00383 / 0.24 ( 28) link_NAG-ASN : angle 2.81779 / 1.82 ( 84) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8277 (m) REVERT: A 441 LEU cc_start: 0.8514 (mt) cc_final: 0.8222 (mp) REVERT: A 559 PHE cc_start: 0.1185 (OUTLIER) cc_final: -0.0582 (m-80) REVERT: A 590 CYS cc_start: 0.5502 (OUTLIER) cc_final: 0.5183 (p) REVERT: A 779 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: A 947 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8290 (mtmm) REVERT: A 1106 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: B 990 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6921 (tm-30) REVERT: C 552 LEU cc_start: 0.9202 (mt) cc_final: 0.8825 (tp) REVERT: C 907 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.8973 (t0) outliers start: 35 outliers final: 19 residues processed: 152 average time/residue: 0.1076 time to fit residues: 26.9822 Evaluate side-chains 123 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 222 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 540 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 450 ASN C 519 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.132759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094843 restraints weight = 44826.795| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.01 r_work: 0.3231 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 19738 Z= 0.252 Angle : 0.673 11.859 26913 Z= 0.343 Chirality : 0.047 0.303 3159 Planarity : 0.004 0.039 3427 Dihedral : 5.772 59.930 2584 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.42 % Allowed : 11.04 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.42 (0.16), residues: 2389 helix: 1.39 (0.21), residues: 656 sheet: -0.44 (0.21), residues: 457 loop : -1.12 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1019 TYR 0.024 0.002 TYR A 904 PHE 0.023 0.002 PHE A 888 TRP 0.009 0.001 TRP A 436 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (19680) covalent geometry : angle 0.64848 / 0.34 (26768) SS BOND : bond 0.00456 / 0.31 ( 29) SS BOND : angle 2.12113 / 1.20 ( 58) hydrogen bonds : bond 0.04746 / 3.01 ( 844) hydrogen bonds : angle 5.81736 / 4.01 ( 2388) link_BETA1-4 : bond 0.00453 / 0.24 ( 1) link_BETA1-4 : angle 1.70146 / 0.92 ( 3) link_NAG-ASN : bond 0.00412 / 0.27 ( 28) link_NAG-ASN : angle 2.81079 / 1.81 ( 84) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8370 (t) REVERT: A 412 PRO cc_start: 0.7955 (Cg_endo) cc_final: 0.7657 (Cg_exo) REVERT: A 559 PHE cc_start: 0.1400 (OUTLIER) cc_final: -0.0323 (m-80) REVERT: A 590 CYS cc_start: 0.5676 (OUTLIER) cc_final: 0.3956 (p) REVERT: A 779 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: A 947 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8469 (mtmm) REVERT: A 1106 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: B 762 GLN cc_start: 0.8681 (pt0) cc_final: 0.8472 (pt0) REVERT: B 990 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7031 (tm-30) REVERT: C 907 ASN cc_start: 0.9350 (OUTLIER) cc_final: 0.8987 (t0) outliers start: 51 outliers final: 32 residues processed: 142 average time/residue: 0.1003 time to fit residues: 24.0151 Evaluate side-chains 131 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 147 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 0.0370 chunk 17 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 86 optimal weight: 0.6980 chunk 238 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.136047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100932 restraints weight = 43738.563| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.44 r_work: 0.3324 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19738 Z= 0.114 Angle : 0.564 7.962 26913 Z= 0.286 Chirality : 0.044 0.264 3159 Planarity : 0.003 0.038 3427 Dihedral : 5.239 59.008 2584 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.52 % Allowed : 12.17 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.04 (0.17), residues: 2389 helix: 1.85 (0.21), residues: 656 sheet: -0.23 (0.22), residues: 463 loop : -0.97 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.021 0.001 TYR C1067 PHE 0.018 0.001 PHE A 400 TRP 0.012 0.001 TRP A 436 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (19680) covalent geometry : angle 0.54425 / 0.28 (26768) SS BOND : bond 0.00319 / 0.22 ( 29) SS BOND : angle 1.49968 / 0.87 ( 58) hydrogen bonds : bond 0.03786 / 2.40 ( 844) hydrogen bonds : angle 5.40671 / 3.72 ( 2388) link_BETA1-4 : bond 0.00349 / 0.18 ( 1) link_BETA1-4 : angle 1.28064 / 0.80 ( 3) link_NAG-ASN : bond 0.00366 / 0.23 ( 28) link_NAG-ASN : angle 2.39735 / 1.54 ( 84) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 VAL cc_start: 0.8277 (t) cc_final: 0.8071 (m) REVERT: A 559 PHE cc_start: 0.1071 (OUTLIER) cc_final: -0.0704 (m-80) REVERT: A 598 ILE cc_start: 0.8998 (mt) cc_final: 0.8780 (mt) REVERT: A 779 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: A 947 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8241 (mtmm) REVERT: A 1019 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7637 (ttp-110) REVERT: B 990 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 266 TYR cc_start: 0.6718 (OUTLIER) cc_final: 0.5281 (m-80) REVERT: C 552 LEU cc_start: 0.9234 (mp) cc_final: 0.8528 (tp) REVERT: C 907 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.8933 (t0) outliers start: 32 outliers final: 19 residues processed: 142 average time/residue: 0.1081 time to fit residues: 25.0654 Evaluate side-chains 122 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 83 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 607 GLN A 655 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B1135 ASN C 519 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.133464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.092920 restraints weight = 44197.548| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.23 r_work: 0.3282 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19738 Z= 0.211 Angle : 0.623 8.764 26913 Z= 0.315 Chirality : 0.046 0.279 3159 Planarity : 0.004 0.038 3427 Dihedral : 5.321 59.801 2582 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.18 % Allowed : 12.17 % Favored : 85.65 % 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 (0.17), residues: 2389 helix: 1.64 (0.21), residues: 655 sheet: -0.27 (0.22), residues: 450 loop : -1.08 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1019 TYR 0.020 0.002 TYR A 904 PHE 0.021 0.002 PHE A 888 TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (19680) covalent geometry : angle 0.60495 / 0.31 (26768) SS BOND : bond 0.00551 / 0.41 ( 29) SS BOND : angle 1.59558 / 0.97 ( 58) hydrogen bonds : bond 0.04432 / 2.80 ( 844) hydrogen bonds : angle 5.58704 / 3.85 ( 2388) link_BETA1-4 : bond 0.00390 / 0.21 ( 1) link_BETA1-4 : angle 1.50679 / 0.81 ( 3) link_NAG-ASN : bond 0.00388 / 0.26 ( 28) link_NAG-ASN : angle 2.44487 / 1.57 ( 84) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 LEU cc_start: 0.9048 (mp) cc_final: 0.8823 (tp) REVERT: A 559 PHE cc_start: 0.1111 (OUTLIER) cc_final: -0.0658 (m-80) REVERT: A 779 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: A 947 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8428 (mtmm) REVERT: A 1106 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: A 1138 TYR cc_start: 0.8725 (t80) cc_final: 0.8510 (t80) REVERT: B 762 GLN cc_start: 0.8618 (pt0) cc_final: 0.8394 (pt0) REVERT: B 990 GLU cc_start: 0.7427 (tm-30) cc_final: 0.6953 (tm-30) REVERT: B 1138 TYR cc_start: 0.7735 (t80) cc_final: 0.7452 (t80) REVERT: C 552 LEU cc_start: 0.9261 (mp) cc_final: 0.8526 (tp) REVERT: C 907 ASN cc_start: 0.9298 (OUTLIER) cc_final: 0.8945 (t0) outliers start: 46 outliers final: 31 residues processed: 138 average time/residue: 0.1041 time to fit residues: 24.1558 Evaluate side-chains 128 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 66 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 224 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.134033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093594 restraints weight = 44053.240| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.23 r_work: 0.3313 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19738 Z= 0.167 Angle : 0.585 8.667 26913 Z= 0.296 Chirality : 0.045 0.265 3159 Planarity : 0.004 0.037 3427 Dihedral : 5.184 58.860 2582 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.99 % Allowed : 12.65 % Favored : 85.36 % 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: -0.18 (0.17), residues: 2389 helix: 1.73 (0.21), residues: 657 sheet: -0.24 (0.22), residues: 452 loop : -1.08 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.020 0.001 TYR A 904 PHE 0.016 0.001 PHE A 400 TRP 0.014 0.001 TRP C 104 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (19680) covalent geometry : angle 0.56789 / 0.29 (26768) SS BOND : bond 0.00418 / 0.30 ( 29) SS BOND : angle 1.46429 / 0.90 ( 58) hydrogen bonds : bond 0.04126 / 2.61 ( 844) hydrogen bonds : angle 5.45380 / 3.75 ( 2388) link_BETA1-4 : bond 0.00544 / 0.29 ( 1) link_BETA1-4 : angle 1.47802 / 0.84 ( 3) link_NAG-ASN : bond 0.00357 / 0.24 ( 28) link_NAG-ASN : angle 2.28026 / 1.46 ( 84) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: A 368 LEU cc_start: 0.8995 (mp) cc_final: 0.8760 (tp) REVERT: A 559 PHE cc_start: 0.1223 (OUTLIER) cc_final: -0.0527 (m-80) REVERT: A 779 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: A 947 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8324 (mtmm) REVERT: A 1138 TYR cc_start: 0.8694 (t80) cc_final: 0.8467 (t80) REVERT: B 762 GLN cc_start: 0.8593 (pt0) cc_final: 0.8356 (pt0) REVERT: B 990 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6906 (tm-30) REVERT: B 1138 TYR cc_start: 0.7750 (t80) cc_final: 0.7463 (t80) REVERT: C 266 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.5214 (m-80) REVERT: C 552 LEU cc_start: 0.9260 (mp) cc_final: 0.8526 (tp) REVERT: C 907 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.8981 (t0) outliers start: 42 outliers final: 29 residues processed: 130 average time/residue: 0.0967 time to fit residues: 21.4717 Evaluate side-chains 128 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 67 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 74 optimal weight: 0.3980 chunk 123 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 138 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 519 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.135046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094938 restraints weight = 43743.579| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.15 r_work: 0.3327 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19738 Z= 0.127 Angle : 0.555 8.721 26913 Z= 0.280 Chirality : 0.044 0.252 3159 Planarity : 0.003 0.038 3427 Dihedral : 4.998 58.684 2582 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.80 % Allowed : 12.65 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.17), residues: 2389 helix: 1.86 (0.21), residues: 663 sheet: -0.16 (0.22), residues: 452 loop : -1.05 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.022 0.001 TYR A 508 PHE 0.017 0.001 PHE A 400 TRP 0.026 0.001 TRP C 104 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (19680) covalent geometry : angle 0.53905 / 0.28 (26768) SS BOND : bond 0.00372 / 0.27 ( 29) SS BOND : angle 1.35576 / 0.83 ( 58) hydrogen bonds : bond 0.03842 / 2.43 ( 844) hydrogen bonds : angle 5.30255 / 3.65 ( 2388) link_BETA1-4 : bond 0.00699 / 0.37 ( 1) link_BETA1-4 : angle 1.41111 / 0.82 ( 3) link_NAG-ASN : bond 0.00339 / 0.22 ( 28) link_NAG-ASN : angle 2.14344 / 1.37 ( 84) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: A 368 LEU cc_start: 0.9029 (mp) cc_final: 0.8816 (tp) REVERT: A 559 PHE cc_start: 0.0906 (OUTLIER) cc_final: -0.0880 (m-80) REVERT: A 779 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: A 947 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8252 (mtmm) REVERT: A 1138 TYR cc_start: 0.8681 (t80) cc_final: 0.8453 (t80) REVERT: B 762 GLN cc_start: 0.8527 (pt0) cc_final: 0.8314 (pt0) REVERT: B 990 GLU cc_start: 0.7377 (tm-30) cc_final: 0.6877 (tm-30) REVERT: B 1138 TYR cc_start: 0.7658 (t80) cc_final: 0.7368 (t80) REVERT: C 266 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: C 552 LEU cc_start: 0.9229 (mp) cc_final: 0.8498 (tp) outliers start: 38 outliers final: 31 residues processed: 138 average time/residue: 0.0973 time to fit residues: 23.4674 Evaluate side-chains 132 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 231 optimal weight: 0.0370 chunk 238 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.136463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101371 restraints weight = 43865.448| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.29 r_work: 0.3346 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19738 Z= 0.102 Angle : 0.530 8.693 26913 Z= 0.267 Chirality : 0.044 0.234 3159 Planarity : 0.003 0.041 3427 Dihedral : 4.723 58.486 2580 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.33 % Allowed : 13.17 % Favored : 85.50 % 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: 0.14 (0.17), residues: 2389 helix: 2.04 (0.21), residues: 663 sheet: -0.03 (0.22), residues: 460 loop : -0.94 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1019 TYR 0.020 0.001 TYR C1067 PHE 0.024 0.001 PHE A 140 TRP 0.031 0.001 TRP C 104 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (19680) covalent geometry : angle 0.51642 / 0.26 (26768) SS BOND : bond 0.00305 / 0.21 ( 29) SS BOND : angle 1.26801 / 0.78 ( 58) hydrogen bonds : bond 0.03475 / 2.20 ( 844) hydrogen bonds : angle 5.11330 / 3.52 ( 2388) link_BETA1-4 : bond 0.00701 / 0.37 ( 1) link_BETA1-4 : angle 1.28644 / 0.79 ( 3) link_NAG-ASN : bond 0.00327 / 0.21 ( 28) link_NAG-ASN : angle 1.93651 / 1.24 ( 84) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7986 (mp10) REVERT: A 947 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8195 (mtmm) REVERT: A 950 ASP cc_start: 0.8682 (t0) cc_final: 0.8456 (t0) REVERT: A 1138 TYR cc_start: 0.8704 (t80) cc_final: 0.8494 (t80) REVERT: B 990 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6912 (tm-30) REVERT: B 1138 TYR cc_start: 0.7628 (t80) cc_final: 0.7359 (t80) REVERT: C 266 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.5499 (m-80) REVERT: C 552 LEU cc_start: 0.9158 (mp) cc_final: 0.8428 (tp) outliers start: 28 outliers final: 24 residues processed: 139 average time/residue: 0.1086 time to fit residues: 24.9865 Evaluate side-chains 124 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 75 optimal weight: 0.9980 chunk 181 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 158 optimal weight: 0.6980 chunk 195 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 954 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.136684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096657 restraints weight = 43749.040| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.27 r_work: 0.3354 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19738 Z= 0.105 Angle : 0.543 8.453 26913 Z= 0.272 Chirality : 0.044 0.236 3159 Planarity : 0.003 0.041 3427 Dihedral : 4.639 56.855 2580 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.56 % Allowed : 13.07 % Favored : 85.36 % 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: 0.17 (0.17), residues: 2389 helix: 2.06 (0.21), residues: 663 sheet: 0.00 (0.23), residues: 448 loop : -0.92 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 408 TYR 0.020 0.001 TYR C1067 PHE 0.018 0.001 PHE A 400 TRP 0.026 0.001 TRP C 104 HIS 0.002 0.000 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (19680) covalent geometry : angle 0.53041 / 0.27 (26768) SS BOND : bond 0.00371 / 0.28 ( 29) SS BOND : angle 1.25944 / 0.77 ( 58) hydrogen bonds : bond 0.03506 / 2.21 ( 844) hydrogen bonds : angle 5.07462 / 3.49 ( 2388) link_BETA1-4 : bond 0.00757 / 0.40 ( 1) link_BETA1-4 : angle 1.33633 / 0.80 ( 3) link_NAG-ASN : bond 0.00308 / 0.20 ( 28) link_NAG-ASN : angle 1.90300 / 1.21 ( 84) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.79 seconds wall clock time: 66 minutes 33.19 seconds (3993.19 seconds total)