Starting phenix.real_space_refine on Wed Oct 28 01:24:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.map" model { file = "/net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fjn_31624/10_2026/7fjn_31624.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 117 5.16 5 C 17116 2.51 5 N 4414 2.21 5 O 5177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26824 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 7691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7691 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 7678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7678 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 7 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "J" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 108} Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Restraints were copied for chains: I, L Time building chain proxies: 6.92, per 1000 atoms: 0.26 Number of scatterers: 26824 At special positions: 0 Unit cell: (189.937, 166.881, 155.902, 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 117 16.00 O 5177 8.00 N 4414 7.00 C 17116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.06 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.16 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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 617 " - pdb=" SG CYS C 649 " distance=2.09 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 717 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6374 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 56 sheets defined 21.1% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 342 removed outlier: 4.398A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.592A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.512A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.133A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.546A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.656A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.562A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 963 removed outlier: 4.253A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.820A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.015A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.148A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.677A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.056A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.502A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.868A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.580A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.589A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.549A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.869A 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: 3.870A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.850A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.923A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.667A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 759 removed outlier: 6.946A pdb=" N SER C 758 " --> pdb=" O GLN C 755 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE C 759 " --> pdb=" O TYR C 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 755 through 759' Processing helix chain 'C' and resid 760 through 783 removed outlier: 4.341A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.616A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.543A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.535A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.581A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.072A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.794A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.672A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.823A 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: 3.646A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.292A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.006A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 357 removed outlier: 4.048A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.890A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.999A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.866A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.207A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.969A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.673A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.564A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.427A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.616A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.623A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.823A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.860A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 720 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 720 removed outlier: 3.644A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.919A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.533A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.343A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.983A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.609A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.971A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.862A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'H' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS H 22 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 59 through 60 removed outlier: 3.519A pdb=" N SER H 59 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 18 through 23 removed outlier: 3.589A pdb=" N CYS I 22 " --> pdb=" O ALA I 79 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP I 73 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 59 through 60 removed outlier: 3.520A pdb=" N SER I 59 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER J 7 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER J 22 " --> pdb=" O SER J 7 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.265A pdb=" N LEU J 11 " --> pdb=" O GLU J 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'J' and resid 30 through 31 removed outlier: 3.626A pdb=" N LYS J 36 " --> pdb=" O TYR J 31 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP J 41 " --> pdb=" O LEU J 53 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N HIS J 55 " --> pdb=" O LEU J 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU J 39 " --> pdb=" O HIS J 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.594A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.264A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.626A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 59 through 60 removed outlier: 6.707A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU L 39 " --> pdb=" O HIS L 55 " (cutoff:3.500A) 1040 hydrogen bonds defined for protein. 2820 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: 6.73 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6697 1.33 - 1.47: 8125 1.47 - 1.61: 12454 1.61 - 1.75: 2 1.75 - 1.89: 145 Bond restraints: 27423 Sorted by residual: bond pdb=" CA GLY L 106 " pdb=" C GLY L 106 " ideal model delta sigma weight residual 1.518 1.626 -0.108 1.48e-02 4.57e+03 5.34e+01 bond pdb=" CA GLY J 106 " pdb=" C GLY J 106 " ideal model delta sigma weight residual 1.518 1.625 -0.108 1.48e-02 4.57e+03 5.31e+01 bond pdb=" N GLY B 648 " pdb=" CA GLY B 648 " ideal model delta sigma weight residual 1.450 1.500 -0.049 1.01e-02 9.80e+03 2.37e+01 bond pdb=" CA CYS B 617 " pdb=" C CYS B 617 " ideal model delta sigma weight residual 1.522 1.589 -0.067 1.39e-02 5.18e+03 2.34e+01 bond pdb=" N CYS B 649 " pdb=" CA CYS B 649 " ideal model delta sigma weight residual 1.457 1.517 -0.059 1.29e-02 6.01e+03 2.11e+01 ... (remaining 27418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 31070 2.17 - 4.35: 5893 4.35 - 6.52: 329 6.52 - 8.70: 29 8.70 - 10.87: 2 Bond angle restraints: 37323 Sorted by residual: angle pdb=" N PRO B 527 " pdb=" CA PRO B 527 " pdb=" C PRO B 527 " ideal model delta sigma weight residual 111.13 121.81 -10.68 1.49e+00 4.50e-01 5.13e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 118.66 -7.96 1.22e+00 6.72e-01 4.26e+01 angle pdb=" N GLY L 106 " pdb=" CA GLY L 106 " pdb=" C GLY L 106 " ideal model delta sigma weight residual 112.25 104.09 8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" N GLY J 106 " pdb=" CA GLY J 106 " pdb=" C GLY J 106 " ideal model delta sigma weight residual 112.25 104.09 8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 118.08 -7.38 1.22e+00 6.72e-01 3.66e+01 ... (remaining 37318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 14922 17.36 - 34.73: 849 34.73 - 52.09: 136 52.09 - 69.45: 69 69.45 - 86.81: 23 Dihedral angle restraints: 15999 sinusoidal: 6075 harmonic: 9924 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.72 73.72 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -14.88 -71.12 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.39 68.39 1 1.00e+01 1.00e-02 6.06e+01 ... (remaining 15996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3071 0.092 - 0.183: 1115 0.183 - 0.274: 130 0.274 - 0.366: 21 0.366 - 0.457: 3 Chirality restraints: 4340 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CA CYS B 617 " pdb=" N CYS B 617 " pdb=" C CYS B 617 " pdb=" CB CYS B 617 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PRO B 986 " pdb=" N PRO B 986 " pdb=" C PRO B 986 " pdb=" CB PRO B 986 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 4337 not shown) Planarity restraints: 4789 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.343 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A1307 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " -0.326 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG A1302 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " -0.070 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " -0.180 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1304 " -0.333 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG C1304 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C1304 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG C1304 " 0.497 2.00e-02 2.50e+03 pdb=" O7 NAG C1304 " -0.071 2.00e-02 2.50e+03 ... (remaining 4786 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 26 2.23 - 2.90: 10164 2.90 - 3.56: 35451 3.56 - 4.23: 62076 4.23 - 4.90: 104703 Nonbonded interactions: 212420 Sorted by model distance: nonbonded pdb=" CD2 PHE B 486 " pdb=" CE2 TYR L 100 " model vdw 1.560 3.640 nonbonded pdb=" OE1 GLN B 498 " pdb=" CE2 TYR B 501 " model vdw 1.579 3.340 nonbonded pdb=" CZ PHE A 456 " pdb=" CG GLU I 54 " model vdw 1.619 3.740 nonbonded pdb=" CD2 PHE B 486 " pdb=" CD2 TYR L 100 " model vdw 1.668 3.640 nonbonded pdb=" CB GLN C 498 " pdb=" CE2 TYR C 501 " model vdw 1.749 3.740 ... (remaining 212415 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 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 168 or (resid 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 676 or resid 690 thro \ ugh 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) o \ r resid 746 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 827 or resid 855 through 866 \ or (resid 867 through 868 and (name N or name CA or name C or name O or name CB \ )) or resid 869 through 1308)) selection = (chain 'B' and (resid 27 through 87 or (resid 88 and (name N or name CA or name \ C or name O or name CB )) or resid 89 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 114 o \ r (resid 115 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 16 through 168 or (resid 169 and (name N or name CA or name C or name O or name \ CB )) or resid 170 through 190 or (resid 191 and (name N or name CA or name C or \ name O or name CB )) or resid 192 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 676 or resid 690 thro \ ugh 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) o \ r resid 746 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 827 or resid 855 through 866 \ or (resid 867 through 868 and (name N or name CA or name C or name O or name CB \ )) or resid 869 through 985 or (resid 986 through 987 and (name N or name CA or \ name C or name O or name CB )) or resid 988 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 95 or (resid 96 through 97 and (na \ me N or name CA or name C or name O or name CB )) or resid 98 through 196 or (re \ sid 197 and (name N or name CA or name C or name O or name CB )) or resid 198 th \ rough 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) \ or resid 215 through 217 or (resid 218 and (name N or name CA or name C or name \ O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name CA o \ r name C or name O or name CB )) or resid 240 through 308 or (resid 309 and (nam \ e N or name CA or name C or name O or name CB )) or resid 310 through 527 or (re \ sid 528 and (name N or name CA or name C or name O or name CB )) or resid 529 th \ rough 811 or resid 813 through 985 or (resid 986 through 987 and (name N or name \ CA or name C or name O or name CB )) or resid 988 through 1141 or (resid 1142 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1143 through 11 \ 44 or (resid 1145 through 1146 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1147 through 1308)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' } 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: 0.010 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.760 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.128 27470 Z= 0.734 Angle : 1.566 15.029 37442 Z= 1.070 Chirality : 0.087 0.457 4340 Planarity : 0.017 0.292 4764 Dihedral : 12.446 86.813 9559 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.50 % Favored : 92.11 % Rotamer: Outliers : 2.63 % Allowed : 3.79 % Favored : 93.59 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.21 (0.13), residues: 3358 helix: -0.24 (0.18), residues: 597 sheet: 0.39 (0.20), residues: 672 loop : -1.44 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 102 TYR 0.096 0.009 TYR A 707 PHE 0.060 0.008 PHE B 927 TRP 0.050 0.006 TRP B 886 HIS 0.016 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.01153 / 0.73 (27423) covalent geometry : angle 1.56027 / 1.07 (37323) SS BOND : bond 0.03124 / 1.53 ( 22) SS BOND : angle 3.51046 / 2.86 ( 44) hydrogen bonds : bond 0.16692 / 10.56 ( 1038) hydrogen bonds : angle 8.69241 / 5.97 ( 2820) link_NAG-ASN : bond 0.00768 / 0.46 ( 25) link_NAG-ASN : angle 2.45004 / 1.47 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 311 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 PHE cc_start: 0.0874 (m-10) cc_final: 0.0358 (m-80) REVERT: I 43 GLN cc_start: -0.3820 (OUTLIER) cc_final: -0.4654 (tt0) REVERT: J 15 VAL cc_start: 0.2425 (OUTLIER) cc_final: 0.2169 (m) REVERT: J 64 VAL cc_start: -0.1875 (OUTLIER) cc_final: -0.2340 (m) REVERT: J 93 TYR cc_start: -0.1781 (OUTLIER) cc_final: -0.2942 (m-80) REVERT: J 111 GLU cc_start: 0.0954 (OUTLIER) cc_final: 0.0642 (pm20) REVERT: L 44 GLN cc_start: 0.3105 (mt0) cc_final: 0.2812 (mp10) outliers start: 77 outliers final: 14 residues processed: 379 average time/residue: 0.1673 time to fit residues: 102.3610 Evaluate side-chains 149 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 43 GLN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 87 ASN A 334 ASN A 409 GLN A 414 GLN A 474 GLN A 487 ASN A1088 HIS A1119 ASN B 52 GLN B 414 GLN B 762 GLN B 978 ASN B1088 HIS C 414 GLN C 474 GLN C 540 ASN C 955 ASN C1135 ASN H 43 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.082279 restraints weight = 115761.284| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.26 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27470 Z= 0.147 Angle : 0.661 11.202 37442 Z= 0.341 Chirality : 0.047 0.291 4340 Planarity : 0.004 0.041 4764 Dihedral : 5.775 59.926 3687 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 1.91 % Allowed : 7.50 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.33 (0.14), residues: 3358 helix: 1.68 (0.21), residues: 590 sheet: 0.41 (0.18), residues: 870 loop : -1.18 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.032 0.002 TYR L 93 PHE 0.026 0.002 PHE A 201 TRP 0.019 0.001 TRP B 64 HIS 0.004 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (27423) covalent geometry : angle 0.64797 / 0.34 (37323) SS BOND : bond 0.01148 / 0.79 ( 22) SS BOND : angle 1.27002 / 0.87 ( 44) hydrogen bonds : bond 0.04842 / 3.10 ( 1038) hydrogen bonds : angle 6.26501 / 4.27 ( 2820) link_NAG-ASN : bond 0.00480 / 0.29 ( 25) link_NAG-ASN : angle 2.83382 / 2.09 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 0.964 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: A 571 ASP cc_start: 0.8035 (t0) cc_final: 0.7810 (t0) REVERT: B 200 TYR cc_start: 0.6508 (m-80) cc_final: 0.6181 (m-10) REVERT: B 204 TYR cc_start: 0.6231 (m-80) cc_final: 0.6019 (m-80) REVERT: B 285 ILE cc_start: 0.7460 (mt) cc_final: 0.7136 (mm) REVERT: B 970 PHE cc_start: 0.8370 (m-80) cc_final: 0.8158 (m-10) REVERT: B 979 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8626 (t0) REVERT: C 557 LYS cc_start: 0.5726 (mttt) cc_final: 0.5451 (mtmt) REVERT: C 1001 LEU cc_start: 0.8850 (tt) cc_final: 0.8642 (tp) REVERT: C 1005 GLN cc_start: 0.8471 (mt0) cc_final: 0.8235 (mt0) REVERT: H 81 MET cc_start: -0.6212 (ttp) cc_final: -0.6415 (ttp) REVERT: J 39 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3607 (tt) REVERT: J 93 TYR cc_start: -0.2014 (OUTLIER) cc_final: -0.2583 (m-80) outliers start: 56 outliers final: 27 residues processed: 181 average time/residue: 0.1446 time to fit residues: 45.6458 Evaluate side-chains 134 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [163, 99, 266, 194, 258, 301, 45, 221, 140, 118, 19] chunk 163 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 266 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 258 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A 913 GLN B 394 ASN B 481 ASN B 762 GLN B 804 GLN B 901 GLN B 913 GLN B 935 GLN C 448 ASN C 901 GLN C 955 ASN C1119 ASN H 43 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.107370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.067091 restraints weight = 113379.046| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.91 r_work: 0.2899 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.5122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 27470 Z= 0.263 Angle : 0.706 20.226 37442 Z= 0.363 Chirality : 0.047 0.242 4340 Planarity : 0.004 0.051 4764 Dihedral : 5.196 56.608 3673 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.56 % Rotamer: Outliers : 1.98 % Allowed : 7.95 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.27 (0.14), residues: 3358 helix: 1.75 (0.21), residues: 611 sheet: 0.34 (0.18), residues: 886 loop : -1.13 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 454 TYR 0.026 0.002 TYR C 495 PHE 0.021 0.002 PHE A 565 TRP 0.029 0.002 TRP L 56 HIS 0.008 0.002 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 (27423) covalent geometry : angle 0.69592 / 0.36 (37323) SS BOND : bond 0.01189 / 0.95 ( 22) SS BOND : angle 1.59427 / 1.18 ( 44) hydrogen bonds : bond 0.05356 / 3.44 ( 1038) hydrogen bonds : angle 5.96513 / 4.09 ( 2820) link_NAG-ASN : bond 0.00484 / 0.27 ( 25) link_NAG-ASN : angle 2.49644 / 1.78 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 100 time to evaluate : 1.199 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: B 189 LEU cc_start: 0.9240 (pp) cc_final: 0.9031 (tp) REVERT: B 200 TYR cc_start: 0.7488 (m-80) cc_final: 0.7123 (m-10) REVERT: B 204 TYR cc_start: 0.6905 (m-80) cc_final: 0.6502 (m-80) REVERT: B 380 TYR cc_start: 0.7588 (t80) cc_final: 0.7316 (t80) REVERT: B 935 GLN cc_start: 0.9454 (OUTLIER) cc_final: 0.8857 (tm-30) REVERT: B 979 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.8996 (t0) REVERT: C 957 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8464 (tm-30) REVERT: C 1111 GLU cc_start: 0.9096 (tm-30) cc_final: 0.8599 (tm-30) REVERT: H 20 MET cc_start: -0.0880 (ptm) cc_final: -0.1429 (ptm) REVERT: J 93 TYR cc_start: -0.1698 (OUTLIER) cc_final: -0.1972 (m-80) REVERT: L 97 TYR cc_start: -0.4170 (OUTLIER) cc_final: -0.4651 (t80) outliers start: 58 outliers final: 29 residues processed: 150 average time/residue: 0.1680 time to fit residues: 42.6519 Evaluate side-chains 108 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 396 TYR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [144, 63, 189, 223, 67, 300, 138, 93, 334, 284, 305] chunk 144 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 300 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 334 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 305 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS B 901 GLN B 955 ASN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS J 6 GLN L 6 GLN L 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.110329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072035 restraints weight = 111323.074| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.21 r_work: 0.2911 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 27470 Z= 0.116 Angle : 0.526 10.274 37442 Z= 0.272 Chirality : 0.043 0.224 4340 Planarity : 0.004 0.046 4764 Dihedral : 4.598 57.375 3669 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.61 % Rotamer: Outliers : 1.40 % Allowed : 9.28 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.07 (0.15), residues: 3358 helix: 2.36 (0.21), residues: 604 sheet: 0.38 (0.17), residues: 881 loop : -0.93 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 319 TYR 0.014 0.001 TYR A1067 PHE 0.016 0.001 PHE A 92 TRP 0.018 0.001 TRP H 36 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (27423) covalent geometry : angle 0.51752 / 0.27 (37323) SS BOND : bond 0.00234 / 0.17 ( 22) SS BOND : angle 1.03766 / 0.85 ( 44) hydrogen bonds : bond 0.04167 / 2.65 ( 1038) hydrogen bonds : angle 5.38436 / 3.68 ( 2820) link_NAG-ASN : bond 0.00199 / 0.11 ( 25) link_NAG-ASN : angle 2.05298 / 1.48 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 PHE cc_start: 0.4795 (m-80) cc_final: 0.3880 (m-10) REVERT: B 54 LEU cc_start: 0.9118 (tp) cc_final: 0.8915 (tp) REVERT: B 200 TYR cc_start: 0.7466 (m-80) cc_final: 0.7092 (m-10) REVERT: B 204 TYR cc_start: 0.7013 (m-80) cc_final: 0.6598 (m-80) REVERT: B 237 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7809 (ptm-80) REVERT: B 265 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.6702 (p90) REVERT: B 380 TYR cc_start: 0.7561 (t80) cc_final: 0.7222 (t80) REVERT: B 571 ASP cc_start: 0.8648 (t0) cc_final: 0.7859 (t0) REVERT: B 935 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8782 (tm-30) REVERT: B 979 ASP cc_start: 0.9274 (OUTLIER) cc_final: 0.8954 (t0) REVERT: C 950 ASP cc_start: 0.9389 (m-30) cc_final: 0.9177 (m-30) REVERT: C 957 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8396 (tm-30) REVERT: H 20 MET cc_start: -0.1156 (ptm) cc_final: -0.1724 (ptm) REVERT: J 93 TYR cc_start: -0.1930 (OUTLIER) cc_final: -0.2166 (m-80) REVERT: L 97 TYR cc_start: -0.4339 (OUTLIER) cc_final: -0.4642 (t80) outliers start: 41 outliers final: 22 residues processed: 124 average time/residue: 0.1560 time to fit residues: 33.3329 Evaluate side-chains 102 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 55 HIS Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [120, 248, 86, 128, 260, 57, 133, 310, 150, 295, 166] chunk 120 optimal weight: 5.9990 chunk 248 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 133 optimal weight: 30.0000 chunk 310 optimal weight: 30.0000 chunk 150 optimal weight: 0.3980 chunk 295 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 913 GLN B 360 ASN B1135 ASN C 498 GLN H 35 HIS L 37 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.110570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072723 restraints weight = 110446.630| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 4.45 r_work: 0.2909 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27470 Z= 0.094 Angle : 0.492 14.192 37442 Z= 0.252 Chirality : 0.042 0.228 4340 Planarity : 0.003 0.047 4764 Dihedral : 4.303 57.500 3668 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 1.57 % Allowed : 9.55 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.27 (0.15), residues: 3358 helix: 2.56 (0.21), residues: 601 sheet: 0.42 (0.17), residues: 880 loop : -0.75 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.015 0.001 TYR A1067 PHE 0.018 0.001 PHE A 201 TRP 0.017 0.001 TRP H 36 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (27423) covalent geometry : angle 0.48551 / 0.25 (37323) SS BOND : bond 0.00205 / 0.13 ( 22) SS BOND : angle 0.77527 / 0.61 ( 44) hydrogen bonds : bond 0.03697 / 2.32 ( 1038) hydrogen bonds : angle 5.02283 / 3.43 ( 2820) link_NAG-ASN : bond 0.00181 / 0.10 ( 25) link_NAG-ASN : angle 1.79478 / 1.27 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 83 time to evaluate : 1.034 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: A 497 PHE cc_start: 0.4757 (m-80) cc_final: 0.3707 (m-10) REVERT: A 1101 HIS cc_start: 0.6277 (OUTLIER) cc_final: 0.5334 (m-70) REVERT: B 54 LEU cc_start: 0.9098 (tp) cc_final: 0.8875 (tp) REVERT: B 189 LEU cc_start: 0.9196 (tp) cc_final: 0.8841 (tp) REVERT: B 200 TYR cc_start: 0.7527 (m-80) cc_final: 0.7147 (m-10) REVERT: B 204 TYR cc_start: 0.7070 (m-80) cc_final: 0.6556 (m-80) REVERT: B 265 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6675 (p90) REVERT: B 380 TYR cc_start: 0.7557 (t80) cc_final: 0.7194 (t80) REVERT: B 571 ASP cc_start: 0.8720 (t0) cc_final: 0.8059 (t0) REVERT: B 979 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.8963 (t0) REVERT: C 957 GLN cc_start: 0.8837 (tp-100) cc_final: 0.8363 (tm-30) REVERT: H 20 MET cc_start: -0.1168 (ptm) cc_final: -0.1672 (ptm) REVERT: J 93 TYR cc_start: -0.1668 (OUTLIER) cc_final: -0.1985 (m-80) REVERT: L 97 TYR cc_start: -0.4138 (OUTLIER) cc_final: -0.4443 (t80) outliers start: 46 outliers final: 26 residues processed: 123 average time/residue: 0.1445 time to fit residues: 30.6101 Evaluate side-chains 101 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 55 HIS Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 39 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [246, 120, 22, 62, 171, 60, 236, 179, 91, 136, 127] chunk 246 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 0.0030 chunk 62 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 236 optimal weight: 20.0000 chunk 179 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 498 GLN A 913 GLN A1088 HIS B 125 ASN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 935 GLN B1048 HIS C 437 ASN H 35 HIS ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN L 37 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.108081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070828 restraints weight = 109214.928| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 4.51 r_work: 0.2791 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.6483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 27470 Z= 0.209 Angle : 0.592 12.870 37442 Z= 0.301 Chirality : 0.044 0.213 4340 Planarity : 0.004 0.047 4764 Dihedral : 4.545 59.726 3668 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 1.57 % Allowed : 10.06 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.22 (0.15), residues: 3358 helix: 2.51 (0.21), residues: 601 sheet: 0.40 (0.17), residues: 891 loop : -0.80 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 214 TYR 0.019 0.001 TYR C1067 PHE 0.013 0.001 PHE C1075 TRP 0.019 0.002 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (27423) covalent geometry : angle 0.58420 / 0.30 (37323) SS BOND : bond 0.00368 / 0.21 ( 22) SS BOND : angle 1.04309 / 0.77 ( 44) hydrogen bonds : bond 0.04654 / 2.98 ( 1038) hydrogen bonds : angle 5.24034 / 3.60 ( 2820) link_NAG-ASN : bond 0.00225 / 0.12 ( 25) link_NAG-ASN : angle 2.13269 / 1.52 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 72 time to evaluate : 0.987 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 497 PHE cc_start: 0.5406 (m-80) cc_final: 0.5145 (m-80) REVERT: A 935 GLN cc_start: 0.9541 (OUTLIER) cc_final: 0.8851 (tm-30) REVERT: A 1101 HIS cc_start: 0.6901 (OUTLIER) cc_final: 0.6063 (m-70) REVERT: B 54 LEU cc_start: 0.9384 (tp) cc_final: 0.9059 (tp) REVERT: B 200 TYR cc_start: 0.7710 (m-80) cc_final: 0.7370 (m-10) REVERT: B 204 TYR cc_start: 0.7396 (m-80) cc_final: 0.6782 (m-80) REVERT: B 380 TYR cc_start: 0.7514 (t80) cc_final: 0.7162 (t80) REVERT: B 935 GLN cc_start: 0.9498 (OUTLIER) cc_final: 0.8939 (tm-30) REVERT: B 979 ASP cc_start: 0.9359 (OUTLIER) cc_final: 0.9061 (t0) REVERT: C 957 GLN cc_start: 0.9020 (tp-100) cc_final: 0.8510 (tm-30) REVERT: H 20 MET cc_start: -0.1291 (ptm) cc_final: -0.1511 (ptm) REVERT: H 28 ARG cc_start: 0.7070 (ptp90) cc_final: 0.5753 (mmm160) REVERT: J 93 TYR cc_start: -0.1514 (OUTLIER) cc_final: -0.1866 (m-80) REVERT: L 97 TYR cc_start: -0.3880 (OUTLIER) cc_final: -0.4324 (t80) outliers start: 46 outliers final: 26 residues processed: 112 average time/residue: 0.1567 time to fit residues: 30.2709 Evaluate side-chains 94 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 62 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 102 ARG Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [225, 147, 14, 165, 322, 300, 89, 83, 43, 316, 70] chunk 225 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 165 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 316 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1088 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN J 6 GLN L 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.109036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071715 restraints weight = 104323.858| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 4.50 r_work: 0.2811 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 27470 Z= 0.139 Angle : 0.509 10.444 37442 Z= 0.260 Chirality : 0.043 0.227 4340 Planarity : 0.003 0.045 4764 Dihedral : 4.318 59.507 3668 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 1.53 % Allowed : 10.40 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.36 (0.15), residues: 3358 helix: 2.71 (0.21), residues: 601 sheet: 0.46 (0.17), residues: 884 loop : -0.72 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 567 TYR 0.016 0.001 TYR A1067 PHE 0.016 0.001 PHE A 201 TRP 0.014 0.001 TRP H 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (27423) covalent geometry : angle 0.50194 / 0.26 (37323) SS BOND : bond 0.00296 / 0.16 ( 22) SS BOND : angle 0.78707 / 0.58 ( 44) hydrogen bonds : bond 0.04026 / 2.54 ( 1038) hydrogen bonds : angle 5.01506 / 3.44 ( 2820) link_NAG-ASN : bond 0.00205 / 0.09 ( 25) link_NAG-ASN : angle 1.93486 / 1.35 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 68 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 PHE cc_start: 0.5546 (m-80) cc_final: 0.5245 (m-80) REVERT: A 935 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.9183 (tm-30) REVERT: A 1101 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6027 (m-70) REVERT: B 54 LEU cc_start: 0.9358 (tp) cc_final: 0.8817 (tp) REVERT: B 88 ASP cc_start: 0.9213 (m-30) cc_final: 0.9009 (p0) REVERT: B 189 LEU cc_start: 0.9287 (tp) cc_final: 0.9035 (mt) REVERT: B 200 TYR cc_start: 0.7687 (m-80) cc_final: 0.7367 (m-10) REVERT: B 204 TYR cc_start: 0.7417 (m-80) cc_final: 0.6820 (m-80) REVERT: B 237 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7909 (ptm160) REVERT: B 380 TYR cc_start: 0.7550 (t80) cc_final: 0.7191 (t80) REVERT: B 935 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.9043 (tt0) REVERT: C 957 GLN cc_start: 0.8985 (tp-100) cc_final: 0.8500 (tm-30) REVERT: H 28 ARG cc_start: 0.6953 (ptp90) cc_final: 0.5680 (mmm160) REVERT: J 81 ILE cc_start: -0.0651 (OUTLIER) cc_final: -0.0968 (mt) REVERT: J 93 TYR cc_start: -0.1465 (OUTLIER) cc_final: -0.1874 (m-80) REVERT: L 38 TYR cc_start: 0.2614 (m-10) cc_final: 0.2404 (m-80) outliers start: 45 outliers final: 26 residues processed: 108 average time/residue: 0.1493 time to fit residues: 28.2599 Evaluate side-chains 98 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [114, 167, 188, 234, 117, 247, 49, 180, 255, 271, 39] chunk 114 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 234 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 255 optimal weight: 0.0770 chunk 271 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 675 GLN A1088 HIS B 334 ASN B 354 ASN B 360 ASN B 762 GLN B 901 GLN C 764 ASN C 957 GLN I 102 ASN L 37 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.104624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066796 restraints weight = 110946.642| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 4.40 r_work: 0.2752 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.7653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 27470 Z= 0.304 Angle : 0.674 9.455 37442 Z= 0.342 Chirality : 0.047 0.218 4340 Planarity : 0.004 0.043 4764 Dihedral : 4.861 59.956 3664 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 1.43 % Allowed : 10.57 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: -0.03 (0.14), residues: 3358 helix: 2.02 (0.21), residues: 620 sheet: 0.28 (0.17), residues: 861 loop : -0.88 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 328 TYR 0.030 0.002 TYR A 200 PHE 0.019 0.002 PHE C1075 TRP 0.021 0.002 TRP H 36 HIS 0.006 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00694 / 0.30 (27423) covalent geometry : angle 0.66478 / 0.34 (37323) SS BOND : bond 0.00283 / 0.18 ( 22) SS BOND : angle 1.20320 / 0.85 ( 44) hydrogen bonds : bond 0.05255 / 3.39 ( 1038) hydrogen bonds : angle 5.53435 / 3.82 ( 2820) link_NAG-ASN : bond 0.00488 / 0.25 ( 25) link_NAG-ASN : angle 2.42177 / 1.69 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 0.729 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: A 935 GLN cc_start: 0.9566 (OUTLIER) cc_final: 0.8943 (tm-30) REVERT: A 1101 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.7274 (m-70) REVERT: B 54 LEU cc_start: 0.9447 (tp) cc_final: 0.9154 (tp) REVERT: B 88 ASP cc_start: 0.9309 (m-30) cc_final: 0.9058 (p0) REVERT: B 200 TYR cc_start: 0.8016 (m-80) cc_final: 0.7587 (m-10) REVERT: B 204 TYR cc_start: 0.7621 (m-80) cc_final: 0.6931 (m-80) REVERT: B 380 TYR cc_start: 0.7688 (t80) cc_final: 0.7330 (t80) REVERT: H 28 ARG cc_start: 0.7091 (ptp90) cc_final: 0.5885 (mmm160) REVERT: J 93 TYR cc_start: -0.1264 (OUTLIER) cc_final: -0.1651 (m-80) REVERT: L 97 TYR cc_start: -0.3501 (OUTLIER) cc_final: -0.3979 (t80) outliers start: 42 outliers final: 27 residues processed: 96 average time/residue: 0.1602 time to fit residues: 26.6869 Evaluate side-chains 86 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [257, 129, 198, 217, 241, 302, 109, 123, 71, 280, 79] chunk 257 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 217 optimal weight: 0.7980 chunk 241 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 71 optimal weight: 2.9990 chunk 280 optimal weight: 0.0370 chunk 79 optimal weight: 2.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1088 HIS B 804 GLN B 901 GLN H 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.106497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069907 restraints weight = 103894.480| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 4.05 r_work: 0.2781 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27470 Z= 0.152 Angle : 0.524 9.421 37442 Z= 0.267 Chirality : 0.043 0.250 4340 Planarity : 0.003 0.044 4764 Dihedral : 4.466 59.858 3664 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 1.19 % Allowed : 10.88 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.20 (0.15), residues: 3358 helix: 2.45 (0.22), residues: 616 sheet: 0.38 (0.17), residues: 874 loop : -0.81 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 577 TYR 0.017 0.001 TYR C1067 PHE 0.015 0.001 PHE A 201 TRP 0.028 0.001 TRP H 36 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (27423) covalent geometry : angle 0.51564 / 0.27 (37323) SS BOND : bond 0.00220 / 0.15 ( 22) SS BOND : angle 0.87741 / 0.64 ( 44) hydrogen bonds : bond 0.04224 / 2.68 ( 1038) hydrogen bonds : angle 5.11653 / 3.53 ( 2820) link_NAG-ASN : bond 0.00167 / 0.09 ( 25) link_NAG-ASN : angle 2.11368 / 1.47 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 59 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.9533 (OUTLIER) cc_final: 0.9212 (tm-30) REVERT: A 1101 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7306 (m-70) REVERT: B 54 LEU cc_start: 0.9390 (tp) cc_final: 0.9074 (tp) REVERT: B 88 ASP cc_start: 0.9266 (m-30) cc_final: 0.9033 (p0) REVERT: B 200 TYR cc_start: 0.7907 (m-80) cc_final: 0.7638 (m-10) REVERT: B 204 TYR cc_start: 0.7557 (m-80) cc_final: 0.6880 (m-80) REVERT: B 237 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8023 (ptm-80) REVERT: B 380 TYR cc_start: 0.7736 (t80) cc_final: 0.7382 (t80) REVERT: C 559 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: H 28 ARG cc_start: 0.7042 (ptp90) cc_final: 0.5914 (mmm160) REVERT: J 93 TYR cc_start: -0.1528 (OUTLIER) cc_final: -0.2072 (m-80) outliers start: 35 outliers final: 27 residues processed: 89 average time/residue: 0.1520 time to fit residues: 23.6258 Evaluate side-chains 88 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 43 GLN Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 55 HIS Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [78, 265, 179, 133, 250, 225, 218, 292, 103, 162, 152] chunk 78 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 225 optimal weight: 0.3980 chunk 218 optimal weight: 0.7980 chunk 292 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1088 HIS L 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.107993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.071468 restraints weight = 97428.260| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 4.40 r_work: 0.2776 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.7866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27470 Z= 0.137 Angle : 0.513 9.017 37442 Z= 0.261 Chirality : 0.043 0.221 4340 Planarity : 0.003 0.045 4764 Dihedral : 4.341 59.775 3664 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 1.23 % Allowed : 11.02 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.26 (0.15), residues: 3358 helix: 2.50 (0.22), residues: 622 sheet: 0.38 (0.17), residues: 875 loop : -0.75 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.018 0.001 TYR B 453 PHE 0.018 0.001 PHE B 168 TRP 0.022 0.001 TRP H 36 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (27423) covalent geometry : angle 0.50586 / 0.26 (37323) SS BOND : bond 0.00205 / 0.13 ( 22) SS BOND : angle 0.79332 / 0.57 ( 44) hydrogen bonds : bond 0.04019 / 2.54 ( 1038) hydrogen bonds : angle 4.99716 / 3.44 ( 2820) link_NAG-ASN : bond 0.00162 / 0.09 ( 25) link_NAG-ASN : angle 1.89801 / 1.31 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6716 Ramachandran restraints generated. 3358 Oldfield, 0 Emsley, 3358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 935 GLN cc_start: 0.9528 (OUTLIER) cc_final: 0.9209 (tm-30) REVERT: A 1101 HIS cc_start: 0.7600 (OUTLIER) cc_final: 0.7289 (m-70) REVERT: B 54 LEU cc_start: 0.9359 (tp) cc_final: 0.9051 (tp) REVERT: B 88 ASP cc_start: 0.9289 (m-30) cc_final: 0.9013 (p0) REVERT: B 200 TYR cc_start: 0.7956 (m-80) cc_final: 0.7508 (m-10) REVERT: B 204 TYR cc_start: 0.7501 (m-80) cc_final: 0.6817 (m-80) REVERT: B 237 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8031 (ptm-80) REVERT: B 380 TYR cc_start: 0.7735 (t80) cc_final: 0.7376 (t80) REVERT: C 559 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: H 28 ARG cc_start: 0.6998 (ptp90) cc_final: 0.5809 (mmm160) REVERT: J 81 ILE cc_start: -0.1109 (OUTLIER) cc_final: -0.1467 (mt) REVERT: J 93 TYR cc_start: -0.1587 (OUTLIER) cc_final: -0.2152 (m-80) REVERT: L 97 TYR cc_start: -0.3271 (OUTLIER) cc_final: -0.3613 (t80) outliers start: 36 outliers final: 25 residues processed: 86 average time/residue: 0.1464 time to fit residues: 22.0950 Evaluate side-chains 86 residues out of total 2987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain J residue 55 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 93 TYR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 55 HIS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 97 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: [156, 90, 311, 200, 36, 167, 256, 67, 261, 252, 286] chunk 156 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 311 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 901 GLN C1048 HIS H 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.103621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.067063 restraints weight = 109374.972| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.24 r_work: 0.2740 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.8275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27470 Z= 0.227 Angle : 0.579 8.954 37442 Z= 0.294 Chirality : 0.044 0.251 4340 Planarity : 0.004 0.045 4764 Dihedral : 4.544 59.035 3662 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 1.19 % Allowed : 11.15 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % 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: 0.12 (0.15), residues: 3358 helix: 2.25 (0.21), residues: 626 sheet: 0.30 (0.17), residues: 875 loop : -0.80 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 102 TYR 0.030 0.001 TYR A 200 PHE 0.016 0.001 PHE A 106 TRP 0.016 0.001 TRP H 36 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (27423) covalent geometry : angle 0.57089 / 0.29 (37323) SS BOND : bond 0.00260 / 0.17 ( 22) SS BOND : angle 0.96209 / 0.68 ( 44) hydrogen bonds : bond 0.04631 / 2.96 ( 1038) hydrogen bonds : angle 5.21495 / 3.60 ( 2820) link_NAG-ASN : bond 0.00255 / 0.15 ( 25) link_NAG-ASN : angle 2.09390 / 1.45 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8700.61 seconds wall clock time: 148 minutes 58.62 seconds (8938.62 seconds total)