Starting phenix.real_space_refine on Sat Jul 4 12:51:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lss_23507/07_2026/7lss_23507.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 91 5.16 5 C 13153 2.51 5 N 3434 2.21 5 O 3904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20582 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 5677 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 37, 'TRANS': 741} Chain breaks: 11 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'ASN:plan1': 9, 'ASP:plan': 15, 'GLU:plan': 11, 'ARG:plan': 6, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 170 Chain: "B" Number of atoms: 7101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7101 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 219} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 9 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 498 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'ASN:plan1': 18, 'ASP:plan': 34, 'GLN:plan1': 10, 'HIS:plan': 2, 'GLU:plan': 21, 'PHE:plan': 3, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 337 Chain: "C" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5496 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 38, 'TRANS': 746} Chain breaks: 11 Unresolved non-hydrogen bonds: 617 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 470 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'ASP:plan': 26, 'GLN:plan1': 10, 'GLU:plan': 26, 'ASN:plan1': 15, 'PHE:plan': 2, 'ARG:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 321 Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 784 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.10, per 1000 atoms: 0.20 Number of scatterers: 20582 At special positions: 0 Unit cell: (124.844, 131.192, 206.31, 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 91 16.00 O 3904 8.00 N 3434 7.00 C 13153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 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 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A1134 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 61 " " NAG A1309 " - " ASN A 282 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 343 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 61 " " NAG D 1 " - " ASN A1098 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN B 717 " " NAG G 1 " - " ASN B1098 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C1098 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 780.6 milliseconds 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5218 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 41 sheets defined 26.5% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 744 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: 3.895A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.488A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.555A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.025A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (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 965 removed outlier: 4.274A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.648A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.542A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.468A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.553A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 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 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.640A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.310A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 4.115A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.650A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.617A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 27C Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.325A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.009A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.705A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.400A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.288A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.175A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.773A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.909A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.909A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB2, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.112A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.798A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 30 removed outlier: 7.354A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.916A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.750A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 167 through 172 removed outlier: 5.305A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.293A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.744A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.532A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.811A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC4, first strand: chain 'B' and resid 655 through 660 removed outlier: 4.961A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.096A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.096A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 788 through 789 removed outlier: 6.225A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.758A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.066A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.650A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.963A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 309 through 319 removed outlier: 5.499A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.019A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.940A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.230A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.223A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET L 47 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 37 " --> pdb=" O LYS L 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.223A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.610A pdb=" N ILE L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE L 75 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AE5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.728A pdb=" N VAL H 35A" --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.07 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6469 1.34 - 1.46: 5191 1.46 - 1.58: 9255 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 21030 Sorted by residual: bond pdb=" SD MET H 82C" pdb=" CE MET H 82C" ideal model delta sigma weight residual 1.791 1.709 0.082 2.50e-02 1.60e+03 1.08e+01 bond pdb=" CB GLN B 901 " pdb=" CG GLN B 901 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.81e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.12e+00 bond pdb=" CG1 ILE B 434 " pdb=" CD1 ILE B 434 " ideal model delta sigma weight residual 1.513 1.398 0.115 3.90e-02 6.57e+02 8.75e+00 bond pdb=" CB PRO A 897 " pdb=" CG PRO A 897 " ideal model delta sigma weight residual 1.492 1.361 0.131 5.00e-02 4.00e+02 6.89e+00 ... (remaining 21025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 27320 2.32 - 4.65: 1275 4.65 - 6.97: 164 6.97 - 9.29: 12 9.29 - 11.62: 3 Bond angle restraints: 28774 Sorted by residual: angle pdb=" N GLY B 446 " pdb=" CA GLY B 446 " pdb=" C GLY B 446 " ideal model delta sigma weight residual 112.04 100.79 11.25 2.02e+00 2.45e-01 3.10e+01 angle pdb=" C TYR L 49 " pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " ideal model delta sigma weight residual 110.42 120.56 -10.14 1.99e+00 2.53e-01 2.60e+01 angle pdb=" N ASN H 82B" pdb=" CA ASN H 82B" pdb=" C ASN H 82B" ideal model delta sigma weight residual 111.02 116.83 -5.81 1.25e+00 6.40e-01 2.16e+01 angle pdb=" CA MET H 82C" pdb=" CB MET H 82C" pdb=" CG MET H 82C" ideal model delta sigma weight residual 114.10 123.25 -9.15 2.00e+00 2.50e-01 2.09e+01 angle pdb=" CA TYR L 49 " pdb=" CB TYR L 49 " pdb=" CG TYR L 49 " ideal model delta sigma weight residual 113.90 121.91 -8.01 1.80e+00 3.09e-01 1.98e+01 ... (remaining 28769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 11261 17.83 - 35.67: 602 35.67 - 53.50: 86 53.50 - 71.34: 19 71.34 - 89.17: 22 Dihedral angle restraints: 11990 sinusoidal: 3915 harmonic: 8075 Sorted by residual: dihedral pdb=" CA CYS A 131 " pdb=" C CYS A 131 " pdb=" N GLU A 132 " pdb=" CA GLU A 132 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO B 57 " pdb=" C PRO B 57 " pdb=" N PHE B 58 " pdb=" CA PHE B 58 " ideal model delta harmonic sigma weight residual -180.00 -150.21 -29.79 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA ILE C1115 " pdb=" C ILE C1115 " pdb=" N THR C1116 " pdb=" CA THR C1116 " ideal model delta harmonic sigma weight residual 180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 11987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.178: 3477 0.178 - 0.356: 19 0.356 - 0.534: 4 0.534 - 0.712: 1 0.712 - 0.889: 1 Chirality restraints: 3502 Sorted by residual: chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.98e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.94e+00 ... (remaining 3499 not shown) Planarity restraints: 3724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 49 " -0.013 2.00e-02 2.50e+03 3.10e-02 1.93e+01 pdb=" CG TYR L 49 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR L 49 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR L 49 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR L 49 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR L 49 " 0.045 2.00e-02 2.50e+03 pdb=" CZ TYR L 49 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR L 49 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1310 " 0.045 2.00e-02 2.50e+03 3.67e-02 1.68e+01 pdb=" C7 NAG B1310 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B1310 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG B1310 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B1310 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 709 " -0.038 2.00e-02 2.50e+03 3.53e-02 1.55e+01 pdb=" CG ASN B 709 " 0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN B 709 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 709 " 0.036 2.00e-02 2.50e+03 pdb=" C1 NAG B1305 " -0.036 2.00e-02 2.50e+03 ... (remaining 3721 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 121 2.57 - 3.16: 18392 3.16 - 3.74: 31368 3.74 - 4.32: 42592 4.32 - 4.90: 71351 Nonbonded interactions: 163824 Sorted by model distance: nonbonded pdb=" OE1 GLN B 580 " pdb=" C8 NAG B1310 " model vdw 1.993 3.460 nonbonded pdb=" O3 NAG D 1 " pdb=" O6 NAG D 2 " model vdw 2.158 3.040 nonbonded pdb=" OG1 THR L 92 " pdb=" O SER L 95 " model vdw 2.198 3.040 nonbonded pdb=" O3 NAG D 1 " pdb=" O5 NAG D 2 " model vdw 2.220 3.040 nonbonded pdb=" NE ARG H 66 " pdb=" OD1 ASN H 82B" model vdw 2.245 3.120 ... (remaining 163819 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 51 or (resid 52 through 54 and (name N or name \ CA or name C or name O or name CB )) or resid 55 through 67 or resid 81 through \ 97 or (resid 98 through 100 and (name N or name CA or name C or name O or name C \ B )) or resid 101 through 131 or (resid 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 or (resid 134 through 138 and (name N or name \ CA or name C or name O or name CB )) or resid 139 through 195 or (resid 196 thro \ ugh 198 and (name N or name CA or name C or name O or name CB )) or resid 199 th \ rough 238 or (resid 239 through 262 and (name N or name CA or name C or name O o \ r name CB )) or resid 265 through 283 or (resid 284 and (name N or name CA or na \ me C or name O or name CB )) or resid 285 through 292 or (resid 293 through 294 \ and (name N or name CA or name C or name O or name CB )) or resid 295 through 30 \ 3 or (resid 304 through 305 and (name N or name CA or name C or name O or name C \ B )) or resid 306 through 309 or (resid 310 and (name N or name CA or name C or \ name O or name CB )) or resid 311 through 318 or (resid 319 through 321 and (nam \ e N or name CA or name C or name O or name CB )) or resid 322 through 323 or (re \ sid 324 through 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 328 or (resid 532 through 534 and (name N or name CA or name C \ or name O or name CB )) or resid 535 or (resid 536 through 537 and (name N or n \ ame CA or name C or name O or name CB )) or resid 538 through 539 or (resid 540 \ and (name N or name CA or name C or name O or name CB )) or resid 541 through 54 \ 5 or (resid 546 and (name N or name CA or name C or name O or name CB )) or resi \ d 547 through 550 or (resid 551 and (name N or name CA or name C or name O or na \ me CB )) or resid 552 through 553 or (resid 554 and (name N or name CA or name C \ or name O or name CB )) or resid 555 or (resid 556 through 558 and (name N or n \ ame CA or name C or name O or name CB )) or resid 559 or (resid 560 and (name N \ or name CA or name C or name O or name CB )) or resid 561 through 570 or (resid \ 571 through 572 and (name N or name CA or name C or name O or name CB )) or resi \ d 573 through 581 or (resid 582 through 583 and (name N or name CA or name C or \ name O or name CB )) or resid 584 or (resid 585 through 586 and (name N or name \ CA or name C or name O or name CB )) or resid 587 or (resid 588 and (name N or n \ ame CA or name C or name O or name CB )) or resid 589 through 613 or (resid 614 \ and (name N or name CA or name C or name O or name CB )) or resid 615 through 61 \ 8 or (resid 619 and (name N or name CA or name C or name O or name CB )) or resi \ d 620 or resid 641 through 653 or (resid 654 and (name N or name CA or name C or \ name O or name CB )) or resid 655 through 676 or (resid 690 and (name N or name \ CA or name C or name O or name CB )) or resid 691 through 697 or (resid 698 and \ (name N or name CA or name C or name O or name CB )) or resid 699 through 703 o \ r (resid 704 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 05 through 724 or (resid 725 and (name N or name CA or name C or name O or name \ CB )) or resid 726 through 736 or (resid 737 and (name N or name CA or name C or \ name O or name CB )) or resid 738 or (resid 739 through 740 and (name N or name \ CA or name C or name O or name CB )) or resid 741 through 744 or (resid 745 and \ (name N or name CA or name C or name O or name CB )) or resid 746 or (resid 747 \ through 748 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 49 through 750 or (resid 751 and (name N or name CA or name C or name O or name \ CB )) or resid 752 through 754 or (resid 755 and (name N or name CA or name C or \ name O or name CB )) or resid 756 through 757 or (resid 758 and (name N or name \ CA or name C or name O or name CB )) or resid 759 through 760 or (resid 761 and \ (name N or name CA or name C or name O or name CB )) or resid 762 through 764 o \ r (resid 765 through 766 and (name N or name CA or name C or name O or name CB ) \ ) or resid 767 through 772 or (resid 773 and (name N or name CA or name C or nam \ e O or name CB )) or resid 774 through 775 or (resid 776 and (name N or name CA \ or name C or name O or name CB )) or resid 777 through 778 or (resid 779 through \ 780 and (name N or name CA or name C or name O or name CB )) or resid 781 throu \ gh 794 or (resid 795 and (name N or name CA or name C or name O or name CB )) or \ resid 796 through 809 or (resid 810 through 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 815 or (resid 816 and (name N or \ name CA or name C or name O or name CB )) or resid 817 through 819 or (resid 820 \ and (name N or name CA or name C or name O or name CB )) or resid 821 through 8 \ 26 or (resid 827 through 855 and (name N or name CA or name C or name O or name \ CB )) or resid 856 through 857 or (resid 858 and (name N or name CA or name C or \ name O or name CB )) or resid 859 or (resid 860 and (name N or name CA or name \ C or name O or name CB )) or resid 861 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 874 o \ r (resid 875 through 876 and (name N or name CA or name C or name O or name CB ) \ ) or resid 877 through 920 or (resid 921 and (name N or name CA or name C or nam \ e O or name CB )) or resid 922 through 932 or (resid 933 through 934 and (name N \ or name CA or name C or name O or name CB )) or resid 935 through 936 or (resid \ 937 through 944 and (name N or name CA or name C or name O or name CB )) or res \ id 945 through 949 or (resid 950 and (name N or name CA or name C or name O or n \ ame CB )) or resid 951 through 973 or (resid 974 through 977 and (name N or name \ CA or name C or name O or name CB )) or resid 978 or (resid 979 and (name N or \ name CA or name C or name O or name CB )) or resid 980 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 9 \ 87 or (resid 988 through 991 and (name N or name CA or name C or name O or name \ CB )) or resid 992 or (resid 993 through 994 and (name N or name CA or name C or \ name O or name CB )) or resid 995 through 1018 or (resid 1019 through 1020 and \ (name N or name CA or name C or name O or name CB )) or resid 1021 through 1030 \ or (resid 1031 and (name N or name CA or name C or name O or name CB )) or resid \ 1032 through 1039 or (resid 1040 through 1041 and (name N or name CA or name C \ or name O or name CB )) or resid 1042 through 1050 or (resid 1051 and (name N or \ name CA or name C or name O or name CB )) or resid 1052 through 1054 or (resid \ 1055 through 1056 and (name N or name CA or name C or name O or name CB )) or re \ sid 1057 through 1059 or (resid 1060 through 1061 and (name N or name CA or name \ C or name O or name CB )) or resid 1062 through 1065 or (resid 1066 and (name N \ or name CA or name C or name O or name CB )) or resid 1067 or (resid 1068 and ( \ name N or name CA or name C or name O or name CB )) or resid 1069 through 1072 o \ r (resid 1073 and (name N or name CA or name C or name O or name CB )) or resid \ 1074 through 1083 or (resid 1084 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1085 or (resid 1086 through 1087 and (name N or name CA or na \ me C or name O or name CB )) or resid 1088 through 1091 or (resid 1092 and (name \ N or name CA or name C or name O or name CB )) or resid 1093 through 1096 or (r \ esid 1097 and (name N or name CA or name C or name O or name CB )) or resid 1098 \ through 1099 or (resid 1100 and (name N or name CA or name C or name O or name \ CB )) or resid 1101 through 1110 or (resid 1111 and (name N or name CA or name C \ or name O or name CB )) or resid 1112 through 1115 or (resid 1116 through 1118 \ and (name N or name CA or name C or name O or name CB )) or resid 1119 through 1 \ 121 or (resid 1122 through 1123 and (name N or name CA or name C or name O or na \ me CB )) or resid 1124 or (resid 1125 and (name N or name CA or name C or name O \ or name CB )) or resid 1126 or (resid 1127 through 1128 and (name N or name CA \ or name C or name O or name CB )) or resid 1129 or (resid 1130 and (name N or na \ me CA or name C or name O or name CB )) or resid 1131 through 1132 or (resid 113 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 1134 or (res \ id 1135 through 1136 and (name N or name CA or name C or name O or name CB )) or \ resid 1137 through 1138 or (resid 1139 and (name N or name CA or name C or name \ O or name CB )) or resid 1140 through 1143 or (resid 1144 and (name N or name C \ A or name C or name O or name CB )) or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 through 32 or (resid 33 and (name N or nam \ e CA or name C or name O or name CB )) or resid 34 through 35 or (resid 36 and ( \ name N or name CA or name C or name O or name CB )) or resid 37 through 41 or (r \ esid 42 and (name N or name CA or name C or name O or name CB )) or resid 43 thr \ ough 44 or (resid 45 through 47 and (name N or name CA or name C or name O or na \ me CB )) or resid 48 through 50 or (resid 51 through 54 and (name N or name CA o \ r name C or name O or name CB )) or resid 55 through 61 or (resid 62 and (name N \ or name CA or name C or name O or name CB )) or resid 63 through 83 or (resid 8 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 85 through 9 \ 9 or (resid 100 and (name N or name CA or name C or name O or name CB )) or resi \ d 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 116 or (resid 117 through 130 and (name N or name CA or name C \ or name O or name CB )) or resid 131 through 140 or (resid 141 and (name N or n \ ame CA or name C or name O or name CB )) or resid 166 through 173 or (resid 187 \ through 188 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 9 or (resid 190 through 191 and (name N or name CA or name C or name O or name C \ B )) or resid 192 through 194 or (resid 195 through 198 and (name N or name CA o \ r name C or name O or name CB )) or resid 199 through 210 or (resid 215 and (nam \ e N or name CA or name C or name O or name CB )) or resid 216 through 220 or (re \ sid 221 through 224 and (name N or name CA or name C or name O or name CB )) or \ resid 225 through 227 or (resid 228 through 229 and (name N or name CA or name C \ or name O or name CB )) or resid 230 or (resid 231 and (name N or name CA or na \ me C or name O or name CB )) or resid 236 through 239 or (resid 240 through 264 \ and (name N or name CA or name C or name O or name CB )) or resid 265 through 27 \ 2 or (resid 273 and (name N or name CA or name C or name O or name CB )) or resi \ d 274 through 289 or (resid 290 and (name N or name CA or name C or name O or na \ me CB )) or resid 291 through 293 or (resid 294 and (name N or name CA or name C \ or name O or name CB )) or resid 295 through 297 or (resid 298 through 299 and \ (name N or name CA or name C or name O or name CB )) or resid 300 through 301 or \ (resid 302 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 3 through 304 or (resid 305 and (name N or name CA or name C or name O or name C \ B )) or resid 306 through 313 or (resid 314 through 315 and (name N or name CA o \ r name C or name O or name CB )) or resid 316 through 319 or (resid 320 through \ 321 and (name N or name CA or name C or name O or name CB )) or resid 322 throug \ h 324 or (resid 325 and (name N or name CA or name C or name O or name CB )) or \ resid 326 through 617 or (resid 618 through 619 and (name N or name CA or name C \ or name O or name CB )) or resid 620 through 818 or (resid 819 through 820 and \ (name N or name CA or name C or name O or name CB )) or resid 821 through 1309)) \ } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } 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=0.52 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.310 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.011 0.131 21105 Z= 0.493 Angle : 1.155 17.259 28966 Z= 0.629 Chirality : 0.064 0.889 3502 Planarity : 0.007 0.063 3688 Dihedral : 12.259 89.169 6673 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 2711 helix: 0.35 (0.19), residues: 610 sheet: -0.06 (0.19), residues: 665 loop : -0.89 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.010 ARG B1039 TYR 0.047 0.006 TYR L 49 PHE 0.042 0.004 PHE B 464 TRP 0.032 0.006 TRP C 886 HIS 0.017 0.004 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.01100 / 0.49 (21030) covalent geometry : angle 1.11018 / 0.62 (28774) SS BOND : bond 0.00531 / 0.35 ( 33) SS BOND : angle 1.99215 / 1.31 ( 66) hydrogen bonds : bond 0.16587 / 11.30 ( 962) hydrogen bonds : angle 8.36383 / 5.82 ( 2652) link_BETA1-4 : bond 0.00551 / 0.36 ( 6) link_BETA1-4 : angle 3.03148 / 1.75 ( 18) link_NAG-ASN : bond 0.00824 / 0.50 ( 36) link_NAG-ASN : angle 5.06876 / 3.17 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7745 (m-80) cc_final: 0.7122 (m-10) REVERT: A 981 LEU cc_start: 0.9630 (tp) cc_final: 0.9308 (pp) REVERT: B 562 PHE cc_start: 0.7156 (t80) cc_final: 0.6452 (t80) REVERT: B 869 MET cc_start: 0.8887 (mtm) cc_final: 0.8649 (ptp) REVERT: B 900 MET cc_start: 0.8473 (mtt) cc_final: 0.8203 (mtt) REVERT: B 902 MET cc_start: 0.8622 (tpp) cc_final: 0.8019 (tpp) REVERT: B 1050 MET cc_start: 0.8463 (ptp) cc_final: 0.7681 (ptp) REVERT: C 190 ARG cc_start: 0.5429 (mtt180) cc_final: 0.5033 (ptp90) REVERT: C 223 LEU cc_start: 0.8856 (mt) cc_final: 0.8316 (mp) REVERT: C 298 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 697 MET cc_start: 0.8177 (ptm) cc_final: 0.7958 (ptm) REVERT: C 699 LEU cc_start: 0.9048 (mt) cc_final: 0.8793 (mt) REVERT: C 796 ASP cc_start: 0.8330 (t0) cc_final: 0.7898 (t0) REVERT: C 819 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8621 (mt-10) REVERT: C 1002 GLN cc_start: 0.9378 (tt0) cc_final: 0.8701 (tp40) REVERT: C 1017 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8886 (tm-30) REVERT: L 26 THR cc_start: 0.7998 (m) cc_final: 0.7771 (p) REVERT: L 78 LEU cc_start: 0.8149 (mt) cc_final: 0.7916 (tp) REVERT: H 56 ASP cc_start: 0.7937 (t0) cc_final: 0.7397 (t0) REVERT: H 71 LYS cc_start: 0.7880 (pttp) cc_final: 0.7517 (ptmt) REVERT: H 72 ASP cc_start: 0.8721 (t0) cc_final: 0.7824 (p0) REVERT: H 82 MET cc_start: 0.7290 (pmm) cc_final: 0.6715 (ptt) REVERT: H 90 TYR cc_start: 0.6316 (m-80) cc_final: 0.5951 (m-10) REVERT: H 97 ILE cc_start: 0.8966 (mm) cc_final: 0.8654 (mm) REVERT: H 98 GLU cc_start: 0.8374 (pt0) cc_final: 0.8117 (tm-30) REVERT: H 105 GLN cc_start: 0.7676 (tp40) cc_final: 0.7398 (pm20) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1470 time to fit residues: 30.1620 Evaluate side-chains 82 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 ASN A 613 GLN B 437 ASN B1135 ASN H 94 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.046432 restraints weight = 87233.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.048050 restraints weight = 42020.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.049139 restraints weight = 26666.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.049846 restraints weight = 19730.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.050302 restraints weight = 16174.543| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21105 Z= 0.140 Angle : 0.663 11.001 28966 Z= 0.341 Chirality : 0.047 0.412 3502 Planarity : 0.004 0.043 3688 Dihedral : 5.821 24.052 2924 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.53 % Allowed : 3.93 % Favored : 95.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2711 helix: 1.90 (0.20), residues: 631 sheet: 0.15 (0.19), residues: 654 loop : -0.49 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1039 TYR 0.031 0.002 TYR L 49 PHE 0.030 0.002 PHE A 201 TRP 0.019 0.002 TRP B 64 HIS 0.005 0.001 HIS H 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (21030) covalent geometry : angle 0.62534 / 0.33 (28774) SS BOND : bond 0.00185 / 0.13 ( 33) SS BOND : angle 0.99389 / 0.65 ( 66) hydrogen bonds : bond 0.04409 / 2.99 ( 962) hydrogen bonds : angle 6.15806 / 4.35 ( 2652) link_BETA1-4 : bond 0.00604 / 0.39 ( 6) link_BETA1-4 : angle 2.09070 / 1.19 ( 18) link_NAG-ASN : bond 0.00526 / 0.35 ( 36) link_NAG-ASN : angle 3.52376 / 2.20 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9171 (mp) cc_final: 0.8918 (mt) REVERT: A 981 LEU cc_start: 0.9635 (tp) cc_final: 0.9342 (pp) REVERT: B 86 PHE cc_start: 0.8088 (t80) cc_final: 0.7735 (t80) REVERT: B 900 MET cc_start: 0.8680 (mtt) cc_final: 0.8415 (mtt) REVERT: C 190 ARG cc_start: 0.5665 (mtt180) cc_final: 0.5219 (mtt90) REVERT: C 223 LEU cc_start: 0.8889 (mt) cc_final: 0.8358 (mp) REVERT: C 298 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7868 (mt-10) REVERT: C 733 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8969 (mtmt) REVERT: C 796 ASP cc_start: 0.8076 (t0) cc_final: 0.7781 (t0) REVERT: C 819 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 1002 GLN cc_start: 0.9262 (tt0) cc_final: 0.8692 (tp40) REVERT: L 17 GLN cc_start: 0.7326 (pt0) cc_final: 0.6655 (pp30) REVERT: L 26 THR cc_start: 0.8186 (m) cc_final: 0.7736 (p) REVERT: L 27 VAL cc_start: 0.7916 (p) cc_final: 0.7477 (p) REVERT: L 32 TYR cc_start: 0.5861 (m-80) cc_final: 0.5328 (m-80) REVERT: L 78 LEU cc_start: 0.7843 (mt) cc_final: 0.7198 (tp) REVERT: H 56 ASP cc_start: 0.8077 (t0) cc_final: 0.7773 (t0) REVERT: H 97 ILE cc_start: 0.8831 (mm) cc_final: 0.8487 (mm) REVERT: H 105 GLN cc_start: 0.8188 (tp40) cc_final: 0.7548 (pm20) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 0.1381 time to fit residues: 25.7360 Evaluate side-chains 86 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 257 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 232 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.067085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.048721 restraints weight = 84254.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050270 restraints weight = 41976.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.051272 restraints weight = 27394.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051949 restraints weight = 20862.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.052387 restraints weight = 17411.325| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21105 Z= 0.149 Angle : 0.602 9.328 28966 Z= 0.307 Chirality : 0.045 0.376 3502 Planarity : 0.004 0.048 3688 Dihedral : 5.218 23.408 2924 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.01 % Allowed : 5.79 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.16), residues: 2711 helix: 2.03 (0.20), residues: 633 sheet: -0.01 (0.19), residues: 684 loop : -0.34 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.018 0.001 TYR L 49 PHE 0.031 0.001 PHE A 201 TRP 0.021 0.002 TRP B 436 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (21030) covalent geometry : angle 0.56978 / 0.30 (28774) SS BOND : bond 0.00222 / 0.17 ( 33) SS BOND : angle 0.89324 / 0.58 ( 66) hydrogen bonds : bond 0.04006 / 2.72 ( 962) hydrogen bonds : angle 5.73219 / 4.05 ( 2652) link_BETA1-4 : bond 0.00333 / 0.19 ( 6) link_BETA1-4 : angle 1.47447 / 0.81 ( 18) link_NAG-ASN : bond 0.00446 / 0.29 ( 36) link_NAG-ASN : angle 3.11505 / 1.95 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9143 (mp) cc_final: 0.8870 (mt) REVERT: A 981 LEU cc_start: 0.9637 (tp) cc_final: 0.9340 (pp) REVERT: B 86 PHE cc_start: 0.8184 (t80) cc_final: 0.7963 (t80) REVERT: B 562 PHE cc_start: 0.7134 (t80) cc_final: 0.6900 (t80) REVERT: B 900 MET cc_start: 0.8785 (mtt) cc_final: 0.8490 (mtt) REVERT: C 223 LEU cc_start: 0.8879 (mt) cc_final: 0.8484 (mp) REVERT: C 298 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7881 (mt-10) REVERT: C 574 ASP cc_start: 0.8382 (t70) cc_final: 0.7847 (t0) REVERT: C 796 ASP cc_start: 0.8217 (t0) cc_final: 0.7925 (t0) REVERT: C 819 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8265 (mt-10) REVERT: C 1002 GLN cc_start: 0.9257 (tt0) cc_final: 0.8861 (tp40) REVERT: L 17 GLN cc_start: 0.7334 (pt0) cc_final: 0.6721 (pp30) REVERT: L 26 THR cc_start: 0.8095 (m) cc_final: 0.7659 (p) REVERT: L 27 VAL cc_start: 0.8009 (p) cc_final: 0.7750 (p) REVERT: L 78 LEU cc_start: 0.7829 (mt) cc_final: 0.7168 (tp) REVERT: H 55 ASP cc_start: 0.8553 (m-30) cc_final: 0.8173 (t0) REVERT: H 97 ILE cc_start: 0.8796 (mm) cc_final: 0.8515 (mm) REVERT: H 105 GLN cc_start: 0.8265 (tp40) cc_final: 0.7564 (pm20) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 0.1334 time to fit residues: 21.9250 Evaluate side-chains 86 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 69 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 69 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 265 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 245 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.067583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.049069 restraints weight = 83020.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050585 restraints weight = 42039.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051575 restraints weight = 27737.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.052202 restraints weight = 21194.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.052585 restraints weight = 17934.452| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21105 Z= 0.157 Angle : 0.581 8.653 28966 Z= 0.296 Chirality : 0.045 0.358 3502 Planarity : 0.004 0.048 3688 Dihedral : 4.860 22.864 2924 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.11 % Allowed : 6.74 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2711 helix: 2.11 (0.21), residues: 628 sheet: 0.03 (0.19), residues: 663 loop : -0.31 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.016 0.001 TYR L 49 PHE 0.033 0.001 PHE A 201 TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (21030) covalent geometry : angle 0.55467 / 0.29 (28774) SS BOND : bond 0.00150 / 0.10 ( 33) SS BOND : angle 0.80715 / 0.52 ( 66) hydrogen bonds : bond 0.03720 / 2.53 ( 962) hydrogen bonds : angle 5.45281 / 3.86 ( 2652) link_BETA1-4 : bond 0.00315 / 0.18 ( 6) link_BETA1-4 : angle 1.35510 / 0.75 ( 18) link_NAG-ASN : bond 0.00407 / 0.27 ( 36) link_NAG-ASN : angle 2.79256 / 1.75 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9159 (mp) cc_final: 0.8880 (mt) REVERT: A 904 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: A 981 LEU cc_start: 0.9634 (tp) cc_final: 0.9324 (pp) REVERT: B 900 MET cc_start: 0.8828 (mtt) cc_final: 0.8528 (mtt) REVERT: C 223 LEU cc_start: 0.8905 (mt) cc_final: 0.8502 (mp) REVERT: C 298 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 574 ASP cc_start: 0.8351 (t70) cc_final: 0.7855 (t0) REVERT: C 796 ASP cc_start: 0.8311 (t0) cc_final: 0.8054 (t0) REVERT: C 819 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8281 (mt-10) REVERT: C 1002 GLN cc_start: 0.9231 (tt0) cc_final: 0.8879 (tp40) REVERT: C 1050 MET cc_start: 0.8393 (ptp) cc_final: 0.7729 (ptp) REVERT: L 17 GLN cc_start: 0.7352 (pt0) cc_final: 0.6766 (pp30) REVERT: L 26 THR cc_start: 0.8145 (m) cc_final: 0.7734 (p) REVERT: L 27 VAL cc_start: 0.7872 (p) cc_final: 0.7580 (p) REVERT: L 78 LEU cc_start: 0.7724 (mt) cc_final: 0.7019 (tp) REVERT: H 55 ASP cc_start: 0.8791 (m-30) cc_final: 0.8097 (t0) REVERT: H 82 MET cc_start: 0.8293 (mmm) cc_final: 0.7607 (mmm) REVERT: H 97 ILE cc_start: 0.8577 (mm) cc_final: 0.8321 (mm) REVERT: H 105 GLN cc_start: 0.8326 (tp40) cc_final: 0.7644 (pm20) outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.1183 time to fit residues: 21.7159 Evaluate side-chains 92 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 69 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 231 optimal weight: 0.5980 chunk 153 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 180 optimal weight: 0.0870 chunk 233 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN C 777 ASN H 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056623 restraints weight = 66618.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057842 restraints weight = 40775.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.058690 restraints weight = 30537.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059286 restraints weight = 25361.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.059572 restraints weight = 22357.238| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21105 Z= 0.096 Angle : 0.533 8.524 28966 Z= 0.272 Chirality : 0.044 0.318 3502 Planarity : 0.004 0.048 3688 Dihedral : 4.534 22.639 2924 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.27 % Allowed : 7.11 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2711 helix: 2.20 (0.21), residues: 628 sheet: 0.27 (0.20), residues: 646 loop : -0.25 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.017 0.001 TYR B 449 PHE 0.028 0.001 PHE A 201 TRP 0.017 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (21030) covalent geometry : angle 0.50961 / 0.27 (28774) SS BOND : bond 0.00111 / 0.07 ( 33) SS BOND : angle 0.70409 / 0.45 ( 66) hydrogen bonds : bond 0.03420 / 2.32 ( 962) hydrogen bonds : angle 5.17775 / 3.67 ( 2652) link_BETA1-4 : bond 0.00373 / 0.22 ( 6) link_BETA1-4 : angle 1.25986 / 0.70 ( 18) link_NAG-ASN : bond 0.00441 / 0.28 ( 36) link_NAG-ASN : angle 2.55195 / 1.61 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9155 (mp) cc_final: 0.8864 (mt) REVERT: A 724 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9200 (m) REVERT: A 902 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.8989 (mmt) REVERT: A 904 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: A 981 LEU cc_start: 0.9631 (tp) cc_final: 0.9311 (pp) REVERT: A 1050 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7310 (mtp) REVERT: B 900 MET cc_start: 0.8707 (mtt) cc_final: 0.8484 (mtt) REVERT: C 223 LEU cc_start: 0.8682 (mt) cc_final: 0.8394 (mp) REVERT: C 298 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 819 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8082 (mt-10) REVERT: C 1002 GLN cc_start: 0.9116 (tt0) cc_final: 0.8894 (tp40) REVERT: L 17 GLN cc_start: 0.6899 (pt0) cc_final: 0.6408 (pp30) REVERT: L 26 THR cc_start: 0.8002 (m) cc_final: 0.7610 (p) REVERT: L 27 VAL cc_start: 0.7536 (p) cc_final: 0.7246 (p) REVERT: L 31 ASN cc_start: 0.8416 (t0) cc_final: 0.8126 (t0) REVERT: L 78 LEU cc_start: 0.7963 (mt) cc_final: 0.7303 (tp) REVERT: H 55 ASP cc_start: 0.8566 (m-30) cc_final: 0.7934 (t0) REVERT: H 77 GLN cc_start: 0.9025 (mt0) cc_final: 0.8787 (mp10) REVERT: H 82 MET cc_start: 0.7523 (mmm) cc_final: 0.6881 (mmm) REVERT: H 105 GLN cc_start: 0.8297 (tp40) cc_final: 0.7740 (pm20) outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 0.1148 time to fit residues: 22.1546 Evaluate side-chains 100 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 56 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 214 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 250 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 777 ASN A 901 GLN B1135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.067793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.049653 restraints weight = 81923.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.051108 restraints weight = 42767.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.052070 restraints weight = 28506.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052704 restraints weight = 21919.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.053066 restraints weight = 18462.189| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21105 Z= 0.165 Angle : 0.553 8.153 28966 Z= 0.283 Chirality : 0.044 0.341 3502 Planarity : 0.004 0.046 3688 Dihedral : 4.501 21.899 2924 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.65 % Allowed : 7.54 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2711 helix: 2.26 (0.21), residues: 630 sheet: 0.18 (0.19), residues: 659 loop : -0.23 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.024 0.001 TYR C1047 PHE 0.031 0.001 PHE A 201 TRP 0.014 0.001 TRP B 64 HIS 0.003 0.001 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (21030) covalent geometry : angle 0.53075 / 0.28 (28774) SS BOND : bond 0.00151 / 0.11 ( 33) SS BOND : angle 0.67940 / 0.43 ( 66) hydrogen bonds : bond 0.03495 / 2.37 ( 962) hydrogen bonds : angle 5.21206 / 3.69 ( 2652) link_BETA1-4 : bond 0.00262 / 0.14 ( 6) link_BETA1-4 : angle 1.19676 / 0.65 ( 18) link_NAG-ASN : bond 0.00353 / 0.22 ( 36) link_NAG-ASN : angle 2.53564 / 1.60 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9137 (mp) cc_final: 0.8848 (mt) REVERT: A 902 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8919 (mmt) REVERT: A 904 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: A 981 LEU cc_start: 0.9619 (tp) cc_final: 0.9330 (pp) REVERT: A 1050 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7373 (mtp) REVERT: B 900 MET cc_start: 0.8772 (mtt) cc_final: 0.8448 (mtt) REVERT: C 298 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7963 (mt-10) REVERT: C 574 ASP cc_start: 0.8381 (t70) cc_final: 0.7912 (t0) REVERT: C 819 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8208 (mt-10) REVERT: C 1002 GLN cc_start: 0.9161 (tt0) cc_final: 0.8924 (tp40) REVERT: C 1050 MET cc_start: 0.8442 (ptp) cc_final: 0.7804 (ptp) REVERT: L 17 GLN cc_start: 0.7308 (pt0) cc_final: 0.6708 (pp30) REVERT: L 26 THR cc_start: 0.8153 (m) cc_final: 0.7732 (p) REVERT: L 27 VAL cc_start: 0.7899 (p) cc_final: 0.7635 (p) REVERT: L 78 LEU cc_start: 0.7960 (mt) cc_final: 0.7238 (tp) REVERT: H 55 ASP cc_start: 0.8722 (m-30) cc_final: 0.8030 (t0) REVERT: H 82 MET cc_start: 0.7605 (mmm) cc_final: 0.7022 (mmm) REVERT: H 105 GLN cc_start: 0.8383 (tp40) cc_final: 0.7739 (pm20) outliers start: 31 outliers final: 21 residues processed: 102 average time/residue: 0.1133 time to fit residues: 19.7667 Evaluate side-chains 102 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 56 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 103 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 209 optimal weight: 0.0270 chunk 123 optimal weight: 0.0000 chunk 8 optimal weight: 30.0000 chunk 210 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 overall best weight: 0.8644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.062708 restraints weight = 85157.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.064292 restraints weight = 42345.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.065387 restraints weight = 27528.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.066129 restraints weight = 20432.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.066639 restraints weight = 16707.417| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21105 Z= 0.108 Angle : 0.526 8.057 28966 Z= 0.269 Chirality : 0.044 0.325 3502 Planarity : 0.003 0.045 3688 Dihedral : 4.352 21.307 2924 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.49 % Allowed : 8.17 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.17), residues: 2711 helix: 2.32 (0.21), residues: 628 sheet: 0.30 (0.20), residues: 654 loop : -0.21 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.016 0.001 TYR L 49 PHE 0.026 0.001 PHE A 201 TRP 0.016 0.001 TRP B 64 HIS 0.004 0.001 HIS H 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (21030) covalent geometry : angle 0.50463 / 0.26 (28774) SS BOND : bond 0.00107 / 0.07 ( 33) SS BOND : angle 0.65839 / 0.42 ( 66) hydrogen bonds : bond 0.03382 / 2.29 ( 962) hydrogen bonds : angle 5.05542 / 3.58 ( 2652) link_BETA1-4 : bond 0.00426 / 0.26 ( 6) link_BETA1-4 : angle 1.17583 / 0.64 ( 18) link_NAG-ASN : bond 0.00389 / 0.24 ( 36) link_NAG-ASN : angle 2.40205 / 1.52 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9143 (mp) cc_final: 0.8833 (mt) REVERT: A 902 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8865 (mmt) REVERT: A 904 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (m-80) REVERT: A 981 LEU cc_start: 0.9624 (tp) cc_final: 0.9304 (pp) REVERT: A 1050 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7285 (mtp) REVERT: B 86 PHE cc_start: 0.7773 (t80) cc_final: 0.7511 (t80) REVERT: B 900 MET cc_start: 0.8743 (mtt) cc_final: 0.8432 (mtt) REVERT: C 298 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7956 (mt-10) REVERT: C 819 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8243 (mt-10) REVERT: C 1002 GLN cc_start: 0.9192 (tt0) cc_final: 0.8901 (tp40) REVERT: L 17 GLN cc_start: 0.7065 (pt0) cc_final: 0.6517 (pp30) REVERT: L 26 THR cc_start: 0.8175 (m) cc_final: 0.7793 (p) REVERT: L 27 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7653 (p) REVERT: L 32 TYR cc_start: 0.6514 (m-80) cc_final: 0.6166 (m-80) REVERT: L 78 LEU cc_start: 0.8184 (mt) cc_final: 0.7547 (tp) REVERT: H 55 ASP cc_start: 0.8737 (m-30) cc_final: 0.8040 (t0) REVERT: H 82 MET cc_start: 0.7762 (mmm) cc_final: 0.7302 (mmm) REVERT: H 83 ASP cc_start: 0.9370 (t0) cc_final: 0.8983 (m-30) outliers start: 28 outliers final: 18 residues processed: 102 average time/residue: 0.1172 time to fit residues: 20.5002 Evaluate side-chains 100 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 1 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 8 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 187 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 257 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 254 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.065369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.047306 restraints weight = 84932.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.048773 restraints weight = 43946.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.049753 restraints weight = 29147.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.050392 restraints weight = 22337.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050803 restraints weight = 18713.413| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21105 Z= 0.245 Angle : 0.620 9.984 28966 Z= 0.316 Chirality : 0.046 0.358 3502 Planarity : 0.004 0.044 3688 Dihedral : 4.616 20.094 2924 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.65 % Allowed : 8.28 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2711 helix: 2.19 (0.21), residues: 629 sheet: 0.09 (0.19), residues: 680 loop : -0.34 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.020 0.002 TYR A 91 PHE 0.038 0.002 PHE B 562 TRP 0.011 0.002 TRP B 64 HIS 0.005 0.002 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.25 (21030) covalent geometry : angle 0.60060 / 0.31 (28774) SS BOND : bond 0.00198 / 0.14 ( 33) SS BOND : angle 0.76532 / 0.48 ( 66) hydrogen bonds : bond 0.03750 / 2.53 ( 962) hydrogen bonds : angle 5.33753 / 3.78 ( 2652) link_BETA1-4 : bond 0.00288 / 0.17 ( 6) link_BETA1-4 : angle 1.24747 / 0.67 ( 18) link_NAG-ASN : bond 0.00388 / 0.25 ( 36) link_NAG-ASN : angle 2.54070 / 1.61 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9175 (mp) cc_final: 0.8903 (mt) REVERT: A 904 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: A 981 LEU cc_start: 0.9608 (tp) cc_final: 0.9303 (pp) REVERT: B 86 PHE cc_start: 0.7873 (t80) cc_final: 0.7570 (t80) REVERT: B 118 LEU cc_start: 0.8473 (tp) cc_final: 0.8040 (mp) REVERT: B 900 MET cc_start: 0.8838 (mtt) cc_final: 0.8564 (mtt) REVERT: C 574 ASP cc_start: 0.8392 (t70) cc_final: 0.7876 (t0) REVERT: C 697 MET cc_start: 0.8433 (mmm) cc_final: 0.8219 (mmm) REVERT: C 819 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8300 (mt-10) REVERT: C 1002 GLN cc_start: 0.9213 (tt0) cc_final: 0.8960 (tp40) REVERT: C 1050 MET cc_start: 0.8518 (ptp) cc_final: 0.8059 (ptp) REVERT: L 17 GLN cc_start: 0.7108 (pt0) cc_final: 0.6504 (pp30) REVERT: L 26 THR cc_start: 0.8185 (m) cc_final: 0.7796 (p) REVERT: L 27 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7788 (p) REVERT: L 32 TYR cc_start: 0.6624 (m-80) cc_final: 0.6267 (m-80) REVERT: L 78 LEU cc_start: 0.8242 (mt) cc_final: 0.7521 (tp) REVERT: H 55 ASP cc_start: 0.8778 (m-30) cc_final: 0.8073 (t0) REVERT: H 82 MET cc_start: 0.7599 (mmm) cc_final: 0.6989 (mmm) REVERT: H 105 GLN cc_start: 0.8315 (tp40) cc_final: 0.7649 (mp10) outliers start: 31 outliers final: 18 residues processed: 95 average time/residue: 0.1178 time to fit residues: 19.3629 Evaluate side-chains 92 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain H residue 1 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 31 optimal weight: 7.9990 chunk 241 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 245 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN H 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.069213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.050767 restraints weight = 80367.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.052191 restraints weight = 42886.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.053122 restraints weight = 29114.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053730 restraints weight = 22644.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.054125 restraints weight = 19255.486| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21105 Z= 0.121 Angle : 0.543 10.097 28966 Z= 0.276 Chirality : 0.044 0.317 3502 Planarity : 0.004 0.045 3688 Dihedral : 4.415 20.075 2924 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.22 % Allowed : 8.65 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2711 helix: 2.32 (0.21), residues: 629 sheet: 0.22 (0.19), residues: 661 loop : -0.28 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1039 TYR 0.016 0.001 TYR L 49 PHE 0.029 0.001 PHE B 562 TRP 0.015 0.001 TRP B 64 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (21030) covalent geometry : angle 0.52243 / 0.27 (28774) SS BOND : bond 0.00117 / 0.08 ( 33) SS BOND : angle 0.70418 / 0.45 ( 66) hydrogen bonds : bond 0.03450 / 2.34 ( 962) hydrogen bonds : angle 5.10062 / 3.61 ( 2652) link_BETA1-4 : bond 0.00404 / 0.23 ( 6) link_BETA1-4 : angle 1.07226 / 0.59 ( 18) link_NAG-ASN : bond 0.00375 / 0.24 ( 36) link_NAG-ASN : angle 2.40418 / 1.53 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9137 (mp) cc_final: 0.8842 (mt) REVERT: A 904 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7335 (m-10) REVERT: A 981 LEU cc_start: 0.9595 (tp) cc_final: 0.9300 (pp) REVERT: B 86 PHE cc_start: 0.7743 (t80) cc_final: 0.7411 (t80) REVERT: B 118 LEU cc_start: 0.8498 (tp) cc_final: 0.8084 (mp) REVERT: B 900 MET cc_start: 0.8771 (mtt) cc_final: 0.8423 (mtt) REVERT: C 819 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8221 (mt-10) REVERT: C 1002 GLN cc_start: 0.9140 (tt0) cc_final: 0.8920 (tp40) REVERT: C 1050 MET cc_start: 0.8453 (ptp) cc_final: 0.7859 (ptp) REVERT: L 17 GLN cc_start: 0.7142 (pt0) cc_final: 0.6543 (pp30) REVERT: L 26 THR cc_start: 0.8196 (m) cc_final: 0.7836 (p) REVERT: L 27 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7658 (p) REVERT: L 32 TYR cc_start: 0.6581 (m-80) cc_final: 0.6235 (m-80) REVERT: L 78 LEU cc_start: 0.8200 (mt) cc_final: 0.7435 (tp) REVERT: H 55 ASP cc_start: 0.8695 (m-30) cc_final: 0.7960 (t0) REVERT: H 82 MET cc_start: 0.7554 (mmm) cc_final: 0.7222 (mmm) REVERT: H 83 ASP cc_start: 0.9482 (t0) cc_final: 0.9032 (m-30) outliers start: 23 outliers final: 17 residues processed: 89 average time/residue: 0.1138 time to fit residues: 17.0867 Evaluate side-chains 90 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 183 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.051778 restraints weight = 78711.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.053132 restraints weight = 42720.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.054043 restraints weight = 29306.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054623 restraints weight = 23031.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.054996 restraints weight = 19702.461| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21105 Z= 0.141 Angle : 0.542 8.182 28966 Z= 0.276 Chirality : 0.044 0.325 3502 Planarity : 0.004 0.047 3688 Dihedral : 4.361 20.068 2924 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.11 % Allowed : 8.76 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.17), residues: 2711 helix: 2.35 (0.21), residues: 629 sheet: 0.20 (0.19), residues: 671 loop : -0.30 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.017 0.001 TYR L 49 PHE 0.028 0.001 PHE B 562 TRP 0.015 0.001 TRP B 64 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (21030) covalent geometry : angle 0.52198 / 0.27 (28774) SS BOND : bond 0.00117 / 0.08 ( 33) SS BOND : angle 0.71552 / 0.45 ( 66) hydrogen bonds : bond 0.03419 / 2.31 ( 962) hydrogen bonds : angle 5.07793 / 3.60 ( 2652) link_BETA1-4 : bond 0.00253 / 0.14 ( 6) link_BETA1-4 : angle 1.03396 / 0.56 ( 18) link_NAG-ASN : bond 0.00341 / 0.21 ( 36) link_NAG-ASN : angle 2.36739 / 1.51 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5422 Ramachandran restraints generated. 2711 Oldfield, 0 Emsley, 2711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 699 LEU cc_start: 0.9103 (mp) cc_final: 0.8806 (mt) REVERT: A 904 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7420 (m-10) REVERT: A 981 LEU cc_start: 0.9598 (tp) cc_final: 0.9299 (pp) REVERT: B 86 PHE cc_start: 0.7786 (t80) cc_final: 0.7480 (t80) REVERT: B 118 LEU cc_start: 0.8443 (tp) cc_final: 0.8047 (mp) REVERT: B 900 MET cc_start: 0.8799 (mtt) cc_final: 0.8464 (mtt) REVERT: C 819 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 1002 GLN cc_start: 0.9160 (tt0) cc_final: 0.8920 (tp40) REVERT: C 1050 MET cc_start: 0.8544 (ptp) cc_final: 0.7938 (ptp) REVERT: L 17 GLN cc_start: 0.7153 (pt0) cc_final: 0.6583 (pp30) REVERT: L 78 LEU cc_start: 0.8164 (mt) cc_final: 0.7376 (tp) REVERT: H 55 ASP cc_start: 0.8701 (m-30) cc_final: 0.7963 (t0) REVERT: H 82 MET cc_start: 0.7519 (mmm) cc_final: 0.7190 (mmm) REVERT: H 83 ASP cc_start: 0.9486 (t0) cc_final: 0.9042 (m-30) REVERT: H 105 GLN cc_start: 0.8451 (tp40) cc_final: 0.7742 (pm20) outliers start: 21 outliers final: 16 residues processed: 88 average time/residue: 0.1112 time to fit residues: 16.9822 Evaluate side-chains 89 residues out of total 2433 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 198 optimal weight: 4.9990 chunk 263 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 202 optimal weight: 0.2980 chunk 162 optimal weight: 0.9990 chunk 199 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.067343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.048507 restraints weight = 80433.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.049929 restraints weight = 43179.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.050878 restraints weight = 29431.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.051500 restraints weight = 23194.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.051914 restraints weight = 19768.563| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21105 Z= 0.199 Angle : 0.578 8.154 28966 Z= 0.295 Chirality : 0.045 0.346 3502 Planarity : 0.004 0.044 3688 Dihedral : 4.484 19.153 2924 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.17 % Allowed : 8.70 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.16), residues: 2711 helix: 2.30 (0.21), residues: 623 sheet: 0.07 (0.19), residues: 694 loop : -0.34 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 509 TYR 0.016 0.002 TYR A 91 PHE 0.027 0.002 PHE B 562 TRP 0.012 0.002 TRP B 64 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (21030) covalent geometry : angle 0.55920 / 0.29 (28774) SS BOND : bond 0.00168 / 0.12 ( 33) SS BOND : angle 0.75223 / 0.47 ( 66) hydrogen bonds : bond 0.03604 / 2.43 ( 962) hydrogen bonds : angle 5.18481 / 3.67 ( 2652) link_BETA1-4 : bond 0.00143 / 0.09 ( 6) link_BETA1-4 : angle 1.01508 / 0.56 ( 18) link_NAG-ASN : bond 0.00343 / 0.22 ( 36) link_NAG-ASN : angle 2.42988 / 1.55 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2946.18 seconds wall clock time: 51 minutes 45.09 seconds (3105.09 seconds total)