Starting phenix.real_space_refine on Mon Aug 25 02:01:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zb5_11145/08_2025/6zb5_11145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zb5_11145/08_2025/6zb5_11145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zb5_11145/08_2025/6zb5_11145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zb5_11145/08_2025/6zb5_11145.map" model { file = "/net/cci-nas-00/data/ceres_data/6zb5_11145/08_2025/6zb5_11145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zb5_11145/08_2025/6zb5_11145.cif" } resolution = 2.85 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= 0.012 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 114 5.16 5 C 15646 2.51 5 N 4043 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24499 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'EIC': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {'EIC': 2, 'NAG': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.24, per 1000 atoms: 0.25 Number of scatterers: 24499 At special positions: 0 Unit cell: (141.75, 135.45, 168, 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 114 16.00 O 4696 8.00 N 4043 7.00 C 15646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.04 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " 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-ASN " NAG A2102 " - " ASN A 343 " " NAG A2104 " - " ASN A 616 " " NAG A2105 " - " ASN A 798 " " NAG B1301 " - " ASN B 798 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 616 " " NAG B1306 " - " ASN B 282 " " NAG B1308 " - " ASN B 17 " " NAG C1401 " - " ASN C 343 " " NAG C1403 " - " ASN C 616 " " NAG C1404 " - " ASN C 798 " " NAG C1405 " - " ASN C1071 " " NAG F 1 " - " ASN A 714 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 873.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 48 sheets defined 24.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.880A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.707A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.528A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 750 Processing helix chain 'C' and resid 754 through 780 removed outlier: 3.902A pdb=" N THR C 758 " --> pdb=" O GLY C 754 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.526A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.337A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 Processing helix chain 'C' and resid 943 through 962 removed outlier: 3.867A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.593A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.578A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (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 349 through 353 removed outlier: 3.882A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.706A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.528A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 750 Processing helix chain 'B' and resid 754 through 780 removed outlier: 3.902A pdb=" N THR B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 846 through 852 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.525A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.337A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 936 Processing helix chain 'B' and resid 943 through 962 removed outlier: 3.866A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.593A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.578A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B1030 " --> pdb=" O MET B1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.881A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.705A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.527A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 750 Processing helix chain 'A' and resid 754 through 780 removed outlier: 3.903A pdb=" N THR A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 905 removed outlier: 3.525A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.336A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 936 Processing helix chain 'A' and resid 943 through 962 removed outlier: 3.867A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.594A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.578A pdb=" N GLU A 987 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.758A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.958A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.733A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.615A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.168A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 698 through 699 removed outlier: 6.255A pdb=" N ALA C 698 " --> pdb=" O ILE A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.566A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C1101 " --> pdb=" O GLN C1110 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN C1103 " --> pdb=" O GLU C1108 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU C1108 " --> pdb=" O GLN C1103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.962A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'C' and resid 784 through 785 Processing sheet with id=AB8, first strand: chain 'C' and resid 1118 through 1119 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.759A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.958A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.240A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.733A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.615A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.168A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.565A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B1101 " --> pdb=" O GLN B1110 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.961A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD5, first strand: chain 'B' and resid 784 through 785 Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1119 Processing sheet with id=AD7, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.759A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.958A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.240A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.734A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.615A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.168A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.566A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1101 " --> pdb=" O GLN A1110 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN A1103 " --> pdb=" O GLU A1108 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU A1108 " --> pdb=" O GLN A1103 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.961A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AF3, first strand: chain 'A' and resid 1118 through 1119 953 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.72 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3987 1.31 - 1.44: 7024 1.44 - 1.57: 13881 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25030 Sorted by residual: bond pdb=" C7 NAG C1406 " pdb=" N2 NAG C1406 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C7 NAG A2101 " pdb=" N2 NAG A2101 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C1 NAG C1406 " pdb=" O5 NAG C1406 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C1 NAG A2101 " pdb=" O5 NAG A2101 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" N ASN B 798 " pdb=" CA ASN B 798 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.27e-02 6.20e+03 9.77e+00 ... (remaining 25025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 33686 3.08 - 6.17: 312 6.17 - 9.25: 17 9.25 - 12.33: 0 12.33 - 15.42: 1 Bond angle restraints: 34016 Sorted by residual: angle pdb=" CA ASN B 798 " pdb=" CB ASN B 798 " pdb=" CG ASN B 798 " ideal model delta sigma weight residual 112.60 128.02 -15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" CB ASN B 798 " pdb=" CG ASN B 798 " pdb=" ND2 ASN B 798 " ideal model delta sigma weight residual 116.40 124.84 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" N GLY B 311 " pdb=" CA GLY B 311 " pdb=" C GLY B 311 " ideal model delta sigma weight residual 110.38 116.82 -6.44 1.28e+00 6.10e-01 2.53e+01 angle pdb=" N GLY C 311 " pdb=" CA GLY C 311 " pdb=" C GLY C 311 " ideal model delta sigma weight residual 110.38 116.81 -6.43 1.28e+00 6.10e-01 2.52e+01 angle pdb=" C ASN B 798 " pdb=" CA ASN B 798 " pdb=" CB ASN B 798 " ideal model delta sigma weight residual 110.79 102.61 8.18 1.63e+00 3.76e-01 2.52e+01 ... (remaining 34011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 14084 27.04 - 54.08: 918 54.08 - 81.12: 128 81.12 - 108.16: 23 108.16 - 135.19: 15 Dihedral angle restraints: 15168 sinusoidal: 6192 harmonic: 8976 Sorted by residual: dihedral pdb=" CA TYR B 704 " pdb=" C TYR B 704 " pdb=" N SER B 705 " pdb=" CA SER B 705 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TYR C 704 " pdb=" C TYR C 704 " pdb=" N SER C 705 " pdb=" CA SER C 705 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TYR A 704 " pdb=" C TYR A 704 " pdb=" N SER A 705 " pdb=" CA SER A 705 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 15165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3902 0.142 - 0.283: 21 0.283 - 0.425: 2 0.425 - 0.566: 3 0.566 - 0.708: 6 Chirality restraints: 3934 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.13e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-02 2.50e+03 4.45e+02 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 3931 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " 0.357 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG B1301 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.138 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.341 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG B1302 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.074 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2102 " 0.334 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A2102 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A2102 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG A2102 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG A2102 " 0.195 2.00e-02 2.50e+03 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 160 2.57 - 3.15: 18216 3.15 - 3.73: 33041 3.73 - 4.32: 50383 4.32 - 4.90: 86371 Nonbonded interactions: 188171 Sorted by model distance: nonbonded pdb=" OD2 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 1.985 3.040 nonbonded pdb=" OD2 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 1.985 3.040 nonbonded pdb=" OD2 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 1.986 3.040 nonbonded pdb=" ND2 ASN C 165 " pdb=" O5 NAG C1402 " model vdw 2.008 3.120 nonbonded pdb=" ND2 ASN B 714 " pdb=" C1 NAG E 1 " model vdw 2.055 3.550 ... (remaining 188166 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' selection = (chain 'B' and resid 15 through 1306) selection = (chain 'C' and resid 15 through 1406) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.000 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.009 0.397 25080 Z= 0.370 Angle : 0.809 18.422 34133 Z= 0.420 Chirality : 0.060 0.708 3934 Planarity : 0.015 0.307 4358 Dihedral : 18.164 135.194 9291 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.76 % Allowed : 20.56 % Favored : 75.69 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: -3.22 (0.13), residues: 3024 helix: -1.71 (0.16), residues: 681 sheet: -0.38 (0.18), residues: 693 loop : -3.27 (0.12), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 78 TYR 0.021 0.002 TYR A 704 PHE 0.016 0.002 PHE A 592 TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A1061 Details of bonding type rmsd covalent geometry : bond 0.00904 (25030) covalent geometry : angle 0.76868 (34016) SS BOND : bond 0.00318 ( 33) SS BOND : angle 1.26761 ( 66) hydrogen bonds : bond 0.12608 ( 947) hydrogen bonds : angle 6.29818 ( 2571) link_BETA1-4 : bond 0.00737 ( 3) link_BETA1-4 : angle 5.46692 ( 9) link_NAG-ASN : bond 0.10689 ( 14) link_NAG-ASN : angle 6.70076 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 317 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: C 187 LYS cc_start: 0.5084 (OUTLIER) cc_final: 0.4316 (ttmt) REVERT: C 207 HIS cc_start: 0.7542 (t-90) cc_final: 0.7156 (m90) REVERT: C 298 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: C 493 GLN cc_start: 0.7806 (mt0) cc_final: 0.7595 (mt0) REVERT: C 801 GLN cc_start: 0.7931 (mt0) cc_final: 0.7592 (mm110) REVERT: B 97 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6256 (pttm) REVERT: B 207 HIS cc_start: 0.7546 (t-90) cc_final: 0.7124 (m90) REVERT: B 567 ARG cc_start: 0.8264 (mmt90) cc_final: 0.7993 (mmt90) REVERT: B 801 GLN cc_start: 0.8096 (mt0) cc_final: 0.7776 (mm110) REVERT: A 128 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6653 (mp) REVERT: A 207 HIS cc_start: 0.7568 (t-90) cc_final: 0.7247 (m90) REVERT: A 346 ARG cc_start: 0.7512 (ttp80) cc_final: 0.7232 (tmt170) REVERT: A 567 ARG cc_start: 0.8352 (mmt90) cc_final: 0.7981 (mmt180) REVERT: A 947 ASP cc_start: 0.7498 (m-30) cc_final: 0.7189 (m-30) REVERT: A 1070 LYS cc_start: 0.7411 (mtpp) cc_final: 0.7205 (tttm) outliers start: 100 outliers final: 31 residues processed: 406 average time/residue: 0.4674 time to fit residues: 223.9763 Evaluate side-chains 289 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.0030 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 137 ASN C 164 ASN C 370 ASN C 540 ASN C 606 ASN C 675 GLN C 916 ASN C 946 GLN C 951 GLN B 125 ASN B 137 ASN B 164 ASN B 603 ASN B 606 ASN B 675 GLN B 687 GLN B 916 ASN B1071 ASN B1098 HIS A 125 ASN A 137 ASN A 606 ASN A 675 GLN A 916 ASN A 951 GLN A1002 GLN A1007 GLN A1071 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.139720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114250 restraints weight = 26818.737| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.63 r_work: 0.2928 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25080 Z= 0.117 Angle : 0.586 11.354 34133 Z= 0.298 Chirality : 0.046 0.274 3934 Planarity : 0.004 0.059 4358 Dihedral : 10.343 114.015 3939 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.97 % Allowed : 20.63 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.14), residues: 3024 helix: 0.29 (0.19), residues: 699 sheet: -0.06 (0.19), residues: 699 loop : -2.71 (0.12), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1104 TYR 0.014 0.001 TYR B1064 PHE 0.020 0.001 PHE B 799 TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00238 (25030) covalent geometry : angle 0.57199 (34016) SS BOND : bond 0.00338 ( 33) SS BOND : angle 1.09563 ( 66) hydrogen bonds : bond 0.05264 ( 947) hydrogen bonds : angle 5.20495 ( 2571) link_BETA1-4 : bond 0.00444 ( 3) link_BETA1-4 : angle 1.85422 ( 9) link_NAG-ASN : bond 0.00772 ( 14) link_NAG-ASN : angle 3.36993 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 259 time to evaluate : 0.945 Fit side-chains REVERT: C 207 HIS cc_start: 0.8060 (t-90) cc_final: 0.7140 (m90) REVERT: C 493 GLN cc_start: 0.8436 (mt0) cc_final: 0.8175 (mt0) REVERT: C 743 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8198 (t) REVERT: C 801 GLN cc_start: 0.8688 (mt0) cc_final: 0.8205 (mm110) REVERT: C 999 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: B 99 ASN cc_start: 0.6535 (m-40) cc_final: 0.6267 (m110) REVERT: B 118 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8293 (tp) REVERT: B 207 HIS cc_start: 0.8032 (t-90) cc_final: 0.7038 (m90) REVERT: B 357 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7596 (ttm170) REVERT: B 613 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7384 (mt0) REVERT: B 801 GLN cc_start: 0.8778 (mt0) cc_final: 0.8309 (mm110) REVERT: B 947 ASP cc_start: 0.8280 (m-30) cc_final: 0.7927 (m-30) REVERT: B 1007 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: A 207 HIS cc_start: 0.8036 (t-90) cc_final: 0.7168 (m90) REVERT: A 346 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7482 (tmt170) REVERT: A 554 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8295 (mm-30) REVERT: A 567 ARG cc_start: 0.8758 (mmt90) cc_final: 0.8468 (mmt90) REVERT: A 947 ASP cc_start: 0.8352 (m-30) cc_final: 0.8025 (m-30) REVERT: A 999 GLN cc_start: 0.8800 (tt0) cc_final: 0.8539 (tt0) REVERT: A 1071 ASN cc_start: 0.7698 (m-40) cc_final: 0.7457 (m110) outliers start: 79 outliers final: 33 residues processed: 318 average time/residue: 0.4940 time to fit residues: 186.7633 Evaluate side-chains 278 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 271 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 236 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN C 951 GLN C1007 GLN B 603 ASN B1071 ASN B1098 HIS A 165 ASN A 234 ASN A 474 GLN A 946 GLN A 951 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.133622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.109334 restraints weight = 27065.642| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.56 r_work: 0.2839 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25080 Z= 0.172 Angle : 0.638 10.946 34133 Z= 0.332 Chirality : 0.048 0.248 3934 Planarity : 0.005 0.068 4358 Dihedral : 9.024 112.673 3899 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.98 % Allowed : 19.09 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.14), residues: 3024 helix: 0.63 (0.20), residues: 696 sheet: 0.18 (0.19), residues: 675 loop : -2.47 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1104 TYR 0.020 0.002 TYR B 279 PHE 0.014 0.002 PHE A 32 TRP 0.011 0.001 TRP B 353 HIS 0.006 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00410 (25030) covalent geometry : angle 0.62547 (34016) SS BOND : bond 0.00501 ( 33) SS BOND : angle 1.53706 ( 66) hydrogen bonds : bond 0.06818 ( 947) hydrogen bonds : angle 5.26883 ( 2571) link_BETA1-4 : bond 0.00405 ( 3) link_BETA1-4 : angle 1.28741 ( 9) link_NAG-ASN : bond 0.00837 ( 14) link_NAG-ASN : angle 3.16709 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 244 time to evaluate : 0.946 Fit side-chains REVERT: C 128 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7230 (mp) REVERT: C 207 HIS cc_start: 0.8277 (t-90) cc_final: 0.7359 (m90) REVERT: C 613 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: C 801 GLN cc_start: 0.8710 (mt0) cc_final: 0.8322 (mm110) REVERT: C 999 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8696 (tm-30) REVERT: C 1110 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8073 (mm110) REVERT: B 118 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8294 (tp) REVERT: B 207 HIS cc_start: 0.8192 (t-90) cc_final: 0.7200 (m90) REVERT: B 234 ASN cc_start: 0.8175 (t0) cc_final: 0.7881 (t0) REVERT: B 357 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7755 (ttm170) REVERT: B 465 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: B 613 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: B 801 GLN cc_start: 0.8805 (mt0) cc_final: 0.8420 (mm110) REVERT: B 947 ASP cc_start: 0.8351 (m-30) cc_final: 0.7959 (m-30) REVERT: B 1007 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8648 (mt0) REVERT: B 1110 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8328 (mm-40) REVERT: A 200 TYR cc_start: 0.8869 (m-80) cc_final: 0.8667 (m-80) REVERT: A 207 HIS cc_start: 0.8168 (t-90) cc_final: 0.7286 (m90) REVERT: A 244 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5611 (pp) REVERT: A 554 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8326 (mm-30) REVERT: A 567 ARG cc_start: 0.8810 (mmt90) cc_final: 0.8497 (mmt90) REVERT: A 613 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7765 (mt0) REVERT: A 755 SER cc_start: 0.7588 (OUTLIER) cc_final: 0.7226 (p) REVERT: A 947 ASP cc_start: 0.8430 (m-30) cc_final: 0.8087 (m-30) REVERT: A 1110 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8306 (mm110) outliers start: 106 outliers final: 52 residues processed: 322 average time/residue: 0.6035 time to fit residues: 228.0331 Evaluate side-chains 295 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 86 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 128 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN C 904 ASN C 951 GLN C1007 GLN B 234 ASN B 603 ASN B 687 GLN B1098 HIS A 234 ASN A 603 ASN A 951 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.135674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.109427 restraints weight = 26819.918| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.69 r_work: 0.2878 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25080 Z= 0.131 Angle : 0.562 10.381 34133 Z= 0.295 Chirality : 0.045 0.299 3934 Planarity : 0.004 0.063 4358 Dihedral : 8.106 116.036 3896 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.34 % Allowed : 19.92 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.14), residues: 3024 helix: 0.98 (0.20), residues: 696 sheet: 0.21 (0.19), residues: 705 loop : -2.31 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1104 TYR 0.017 0.001 TYR A 901 PHE 0.014 0.001 PHE A 32 TRP 0.010 0.001 TRP C 436 HIS 0.007 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00295 (25030) covalent geometry : angle 0.54919 (34016) SS BOND : bond 0.00331 ( 33) SS BOND : angle 1.31019 ( 66) hydrogen bonds : bond 0.05758 ( 947) hydrogen bonds : angle 5.09897 ( 2571) link_BETA1-4 : bond 0.00196 ( 3) link_BETA1-4 : angle 1.02035 ( 9) link_NAG-ASN : bond 0.00750 ( 14) link_NAG-ASN : angle 3.00790 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 241 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.8178 (t-90) cc_final: 0.7288 (m90) REVERT: C 465 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: C 613 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7454 (mt0) REVERT: C 801 GLN cc_start: 0.8701 (mt0) cc_final: 0.8234 (mm110) REVERT: C 999 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8634 (tm-30) REVERT: C 1110 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8021 (mm110) REVERT: B 207 HIS cc_start: 0.7982 (t-90) cc_final: 0.7082 (m90) REVERT: B 321 GLN cc_start: 0.8404 (mm110) cc_final: 0.8075 (mm-40) REVERT: B 357 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7620 (ttm170) REVERT: B 613 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: B 801 GLN cc_start: 0.8741 (mt0) cc_final: 0.8333 (mm110) REVERT: B 947 ASP cc_start: 0.8194 (m-30) cc_final: 0.7756 (m-30) REVERT: B 1007 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8606 (mt0) REVERT: B 1110 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: A 200 TYR cc_start: 0.8816 (m-80) cc_final: 0.8590 (m-80) REVERT: A 207 HIS cc_start: 0.8117 (t-90) cc_final: 0.7254 (m90) REVERT: A 234 ASN cc_start: 0.8266 (t0) cc_final: 0.7950 (t0) REVERT: A 465 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8460 (tt0) REVERT: A 554 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8217 (mm-30) REVERT: A 567 ARG cc_start: 0.8748 (mmt90) cc_final: 0.8448 (mmt90) REVERT: A 613 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: A 755 SER cc_start: 0.7230 (OUTLIER) cc_final: 0.7009 (p) REVERT: A 947 ASP cc_start: 0.8246 (m-30) cc_final: 0.7774 (m-30) REVERT: A 1110 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8214 (mm110) outliers start: 89 outliers final: 45 residues processed: 305 average time/residue: 0.6205 time to fit residues: 221.4223 Evaluate side-chains 283 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 226 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 225 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 302 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 247 optimal weight: 20.0000 chunk 54 optimal weight: 0.6980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN C1007 GLN B 603 ASN B1098 HIS A 603 ASN A 951 GLN A1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.132399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.106698 restraints weight = 26902.317| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.63 r_work: 0.2851 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25080 Z= 0.191 Angle : 0.643 10.605 34133 Z= 0.339 Chirality : 0.048 0.312 3934 Planarity : 0.005 0.068 4358 Dihedral : 8.295 119.815 3893 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.13 % Allowed : 19.54 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.14), residues: 3024 helix: 0.76 (0.20), residues: 696 sheet: 0.22 (0.19), residues: 705 loop : -2.33 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C1104 TYR 0.021 0.002 TYR C 704 PHE 0.016 0.002 PHE A 32 TRP 0.011 0.002 TRP B 353 HIS 0.008 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00460 (25030) covalent geometry : angle 0.63047 (34016) SS BOND : bond 0.00515 ( 33) SS BOND : angle 1.67162 ( 66) hydrogen bonds : bond 0.07116 ( 947) hydrogen bonds : angle 5.30899 ( 2571) link_BETA1-4 : bond 0.00189 ( 3) link_BETA1-4 : angle 1.28048 ( 9) link_NAG-ASN : bond 0.00813 ( 14) link_NAG-ASN : angle 3.10168 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 236 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: C 128 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7173 (mp) REVERT: C 207 HIS cc_start: 0.8184 (t-90) cc_final: 0.7323 (m90) REVERT: C 357 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7644 (ttm170) REVERT: C 613 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: C 801 GLN cc_start: 0.8621 (mt0) cc_final: 0.8169 (mm110) REVERT: C 999 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: C 1110 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8020 (mm110) REVERT: B 118 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8204 (tp) REVERT: B 207 HIS cc_start: 0.7926 (t-90) cc_final: 0.7034 (m90) REVERT: B 239 GLN cc_start: 0.8931 (tt0) cc_final: 0.8659 (tt0) REVERT: B 244 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5550 (pp) REVERT: B 321 GLN cc_start: 0.8439 (mm110) cc_final: 0.8112 (mm-40) REVERT: B 357 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7611 (ttm170) REVERT: B 465 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: B 613 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: B 730 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8250 (mtmt) REVERT: B 801 GLN cc_start: 0.8653 (mt0) cc_final: 0.8224 (mm110) REVERT: B 947 ASP cc_start: 0.8322 (m-30) cc_final: 0.7887 (m-30) REVERT: B 1007 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (mt0) REVERT: B 1110 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8171 (mm-40) REVERT: A 52 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: A 200 TYR cc_start: 0.8909 (m-80) cc_final: 0.8681 (m-80) REVERT: A 207 HIS cc_start: 0.8049 (t-90) cc_final: 0.7141 (m90) REVERT: A 244 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5847 (pp) REVERT: A 465 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: A 554 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: A 567 ARG cc_start: 0.8738 (mmt90) cc_final: 0.8408 (mmt90) REVERT: A 613 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: A 755 SER cc_start: 0.7563 (OUTLIER) cc_final: 0.7203 (p) REVERT: A 947 ASP cc_start: 0.8271 (m-30) cc_final: 0.7791 (m-30) REVERT: A 1110 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8200 (mm110) outliers start: 110 outliers final: 64 residues processed: 319 average time/residue: 0.6158 time to fit residues: 229.8811 Evaluate side-chains 310 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 226 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 92 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 267 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 675 GLN C 687 GLN C 951 GLN C1007 GLN B 603 ASN B1098 HIS A 603 ASN A 951 GLN A1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.133910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107574 restraints weight = 26890.993| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.67 r_work: 0.2849 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25080 Z= 0.146 Angle : 0.583 10.775 34133 Z= 0.309 Chirality : 0.046 0.313 3934 Planarity : 0.005 0.065 4358 Dihedral : 8.053 118.165 3893 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.83 % Allowed : 19.84 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.14), residues: 3024 helix: 0.91 (0.20), residues: 696 sheet: 0.26 (0.19), residues: 705 loop : -2.27 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1104 TYR 0.020 0.002 TYR A 901 PHE 0.014 0.002 PHE A 32 TRP 0.011 0.001 TRP C 436 HIS 0.009 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00337 (25030) covalent geometry : angle 0.57087 (34016) SS BOND : bond 0.00370 ( 33) SS BOND : angle 1.38043 ( 66) hydrogen bonds : bond 0.06241 ( 947) hydrogen bonds : angle 5.19631 ( 2571) link_BETA1-4 : bond 0.00238 ( 3) link_BETA1-4 : angle 1.09357 ( 9) link_NAG-ASN : bond 0.00753 ( 14) link_NAG-ASN : angle 3.07645 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 239 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.8164 (t-90) cc_final: 0.7198 (m90) REVERT: C 357 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7663 (ttm170) REVERT: C 613 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: C 801 GLN cc_start: 0.8653 (mt0) cc_final: 0.8222 (mm110) REVERT: C 999 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8639 (tm-30) REVERT: C 1110 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8072 (mm110) REVERT: B 118 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8224 (tp) REVERT: B 207 HIS cc_start: 0.7953 (t-90) cc_final: 0.7031 (m90) REVERT: B 239 GLN cc_start: 0.8911 (tt0) cc_final: 0.8642 (tt0) REVERT: B 244 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5530 (pp) REVERT: B 321 GLN cc_start: 0.8528 (mm110) cc_final: 0.8206 (mm-40) REVERT: B 357 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7622 (ttm170) REVERT: B 465 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: B 730 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8223 (mtmt) REVERT: B 801 GLN cc_start: 0.8681 (mt0) cc_final: 0.8261 (mm110) REVERT: B 947 ASP cc_start: 0.8320 (m-30) cc_final: 0.7921 (m-30) REVERT: B 1007 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (mt0) REVERT: B 1110 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8192 (mm-40) REVERT: A 200 TYR cc_start: 0.8902 (m-80) cc_final: 0.8640 (m-80) REVERT: A 207 HIS cc_start: 0.8093 (t-90) cc_final: 0.7192 (m90) REVERT: A 244 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5851 (pp) REVERT: A 465 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: A 554 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8293 (mm-30) REVERT: A 567 ARG cc_start: 0.8765 (mmt90) cc_final: 0.8439 (mmt90) REVERT: A 613 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: A 755 SER cc_start: 0.7379 (OUTLIER) cc_final: 0.7106 (p) REVERT: A 947 ASP cc_start: 0.8255 (m-30) cc_final: 0.7774 (m-30) REVERT: A 1110 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8224 (mm110) outliers start: 102 outliers final: 59 residues processed: 314 average time/residue: 0.5891 time to fit residues: 217.7966 Evaluate side-chains 303 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 228 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 183 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 174 optimal weight: 0.0070 chunk 269 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN C1007 GLN B 603 ASN B1098 HIS A 603 ASN A 951 GLN A1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.106907 restraints weight = 26988.085| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.62 r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25080 Z= 0.185 Angle : 0.631 10.761 34133 Z= 0.335 Chirality : 0.048 0.322 3934 Planarity : 0.005 0.067 4358 Dihedral : 8.125 120.101 3893 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.06 % Allowed : 19.77 % Favored : 76.17 % 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 aren not related in a simple way. whole: -1.34 (0.14), residues: 3024 helix: 0.76 (0.20), residues: 696 sheet: 0.26 (0.19), residues: 705 loop : -2.29 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1104 TYR 0.020 0.002 TYR A 901 PHE 0.016 0.002 PHE A1118 TRP 0.011 0.001 TRP C 436 HIS 0.010 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00447 (25030) covalent geometry : angle 0.61903 (34016) SS BOND : bond 0.00479 ( 33) SS BOND : angle 1.57907 ( 66) hydrogen bonds : bond 0.06935 ( 947) hydrogen bonds : angle 5.29058 ( 2571) link_BETA1-4 : bond 0.00205 ( 3) link_BETA1-4 : angle 1.26494 ( 9) link_NAG-ASN : bond 0.00811 ( 14) link_NAG-ASN : angle 3.05845 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 239 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: C 326 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7704 (mp) REVERT: C 357 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7629 (ttm170) REVERT: C 465 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: C 613 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7517 (mt0) REVERT: C 801 GLN cc_start: 0.8622 (mt0) cc_final: 0.8170 (mm110) REVERT: C 999 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8610 (tm-30) REVERT: C 1110 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8022 (mm110) REVERT: B 118 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8194 (tp) REVERT: B 207 HIS cc_start: 0.7936 (t-90) cc_final: 0.7121 (m90) REVERT: B 239 GLN cc_start: 0.8905 (tt0) cc_final: 0.8617 (tt0) REVERT: B 244 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5508 (pp) REVERT: B 321 GLN cc_start: 0.8541 (mm110) cc_final: 0.8219 (mm-40) REVERT: B 357 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7560 (ttm170) REVERT: B 465 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: B 613 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7481 (mt0) REVERT: B 730 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8309 (mtmt) REVERT: B 801 GLN cc_start: 0.8631 (mt0) cc_final: 0.8199 (mm110) REVERT: B 947 ASP cc_start: 0.8308 (m-30) cc_final: 0.7887 (m-30) REVERT: B 1007 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: B 1110 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8174 (mm-40) REVERT: A 200 TYR cc_start: 0.8917 (m-80) cc_final: 0.8693 (m-80) REVERT: A 207 HIS cc_start: 0.8085 (t-90) cc_final: 0.7162 (m90) REVERT: A 244 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5871 (pp) REVERT: A 465 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: A 554 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8256 (mm-30) REVERT: A 567 ARG cc_start: 0.8737 (mmt90) cc_final: 0.8515 (mmt90) REVERT: A 613 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: A 755 SER cc_start: 0.7534 (OUTLIER) cc_final: 0.7191 (p) REVERT: A 875 LEU cc_start: 0.9074 (mm) cc_final: 0.8734 (mt) REVERT: A 947 ASP cc_start: 0.8243 (m-30) cc_final: 0.7778 (m-30) REVERT: A 1110 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8199 (mm110) outliers start: 108 outliers final: 69 residues processed: 317 average time/residue: 0.5959 time to fit residues: 221.2818 Evaluate side-chains 319 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 235 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 272 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 233 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 207 HIS C 951 GLN C1007 GLN B 603 ASN B1098 HIS A 675 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.105655 restraints weight = 26886.705| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.67 r_work: 0.2809 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25080 Z= 0.185 Angle : 0.632 10.786 34133 Z= 0.336 Chirality : 0.048 0.316 3934 Planarity : 0.005 0.068 4358 Dihedral : 8.113 120.420 3893 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.83 % Allowed : 20.14 % Favored : 76.02 % 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 aren not related in a simple way. whole: -1.35 (0.14), residues: 3024 helix: 0.74 (0.20), residues: 696 sheet: 0.26 (0.19), residues: 705 loop : -2.29 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1104 TYR 0.025 0.002 TYR A 901 PHE 0.015 0.002 PHE A1118 TRP 0.012 0.001 TRP C 436 HIS 0.012 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00446 (25030) covalent geometry : angle 0.61984 (34016) SS BOND : bond 0.00474 ( 33) SS BOND : angle 1.56286 ( 66) hydrogen bonds : bond 0.06933 ( 947) hydrogen bonds : angle 5.30108 ( 2571) link_BETA1-4 : bond 0.00156 ( 3) link_BETA1-4 : angle 1.23879 ( 9) link_NAG-ASN : bond 0.00772 ( 14) link_NAG-ASN : angle 3.10152 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 234 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.8184 (t-90) cc_final: 0.7098 (m90) REVERT: C 326 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7736 (mp) REVERT: C 357 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.7655 (ttm170) REVERT: C 465 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: C 613 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7577 (mt0) REVERT: C 801 GLN cc_start: 0.8702 (mt0) cc_final: 0.8256 (mm110) REVERT: C 999 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: C 1110 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8035 (mm110) REVERT: B 207 HIS cc_start: 0.7978 (t-90) cc_final: 0.7131 (m90) REVERT: B 239 GLN cc_start: 0.8931 (tt0) cc_final: 0.8655 (tt0) REVERT: B 244 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5481 (pp) REVERT: B 321 GLN cc_start: 0.8580 (mm110) cc_final: 0.8266 (mm-40) REVERT: B 357 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7671 (ttm170) REVERT: B 465 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: B 730 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8244 (mtmt) REVERT: B 801 GLN cc_start: 0.8713 (mt0) cc_final: 0.8286 (mm110) REVERT: B 947 ASP cc_start: 0.8402 (m-30) cc_final: 0.8017 (m-30) REVERT: B 1007 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8694 (mt0) REVERT: B 1110 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8211 (mm-40) REVERT: A 200 TYR cc_start: 0.8945 (m-80) cc_final: 0.8724 (m-80) REVERT: A 207 HIS cc_start: 0.8119 (t-90) cc_final: 0.7160 (m90) REVERT: A 244 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5846 (pp) REVERT: A 465 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: A 554 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8330 (mm-30) REVERT: A 567 ARG cc_start: 0.8790 (mmt90) cc_final: 0.8567 (mmt90) REVERT: A 613 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: A 755 SER cc_start: 0.7584 (OUTLIER) cc_final: 0.7238 (p) REVERT: A 947 ASP cc_start: 0.8363 (m-30) cc_final: 0.7917 (m-30) REVERT: A 1110 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8244 (mm110) outliers start: 102 outliers final: 70 residues processed: 311 average time/residue: 0.4928 time to fit residues: 181.1337 Evaluate side-chains 318 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 231 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 76 optimal weight: 7.9990 chunk 208 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 137 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 234 ASN C 951 GLN C1007 GLN B 603 ASN B1098 HIS A 675 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.112052 restraints weight = 27083.758| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.61 r_work: 0.2932 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25080 Z= 0.106 Angle : 0.515 11.169 34133 Z= 0.273 Chirality : 0.044 0.305 3934 Planarity : 0.004 0.061 4358 Dihedral : 7.508 112.820 3893 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.56 % Allowed : 21.50 % Favored : 75.95 % 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 aren not related in a simple way. whole: -1.02 (0.14), residues: 3024 helix: 1.25 (0.20), residues: 696 sheet: 0.29 (0.19), residues: 705 loop : -2.11 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1104 TYR 0.021 0.001 TYR A 901 PHE 0.016 0.001 PHE C 830 TRP 0.012 0.001 TRP C 436 HIS 0.011 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00225 (25030) covalent geometry : angle 0.50344 (34016) SS BOND : bond 0.00218 ( 33) SS BOND : angle 1.00249 ( 66) hydrogen bonds : bond 0.04948 ( 947) hydrogen bonds : angle 5.00109 ( 2571) link_BETA1-4 : bond 0.00247 ( 3) link_BETA1-4 : angle 1.03128 ( 9) link_NAG-ASN : bond 0.00633 ( 14) link_NAG-ASN : angle 2.95910 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 357 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: C 465 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: C 586 ASP cc_start: 0.8453 (m-30) cc_final: 0.8233 (m-30) REVERT: C 613 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: C 801 GLN cc_start: 0.8574 (mt0) cc_final: 0.8104 (mm110) REVERT: C 999 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8515 (tm-30) REVERT: C 1110 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8027 (mm110) REVERT: B 207 HIS cc_start: 0.7866 (t-90) cc_final: 0.7020 (m90) REVERT: B 239 GLN cc_start: 0.8803 (tt0) cc_final: 0.8524 (tt0) REVERT: B 244 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5415 (pp) REVERT: B 321 GLN cc_start: 0.8501 (mm110) cc_final: 0.8197 (mm-40) REVERT: B 357 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7506 (ttm170) REVERT: B 801 GLN cc_start: 0.8616 (mt0) cc_final: 0.8161 (mm110) REVERT: B 947 ASP cc_start: 0.8111 (m-30) cc_final: 0.7656 (m-30) REVERT: B 1007 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: B 1110 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8138 (mm-40) REVERT: A 200 TYR cc_start: 0.8801 (m-80) cc_final: 0.8546 (m-80) REVERT: A 207 HIS cc_start: 0.7970 (t-90) cc_final: 0.7084 (m90) REVERT: A 244 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5715 (pp) REVERT: A 554 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: A 567 ARG cc_start: 0.8697 (mmt90) cc_final: 0.8343 (mmt90) REVERT: A 1110 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8164 (mm110) outliers start: 68 outliers final: 40 residues processed: 294 average time/residue: 0.5185 time to fit residues: 178.1105 Evaluate side-chains 282 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 97 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 951 GLN C1007 GLN B 603 ASN B 946 GLN B1098 HIS A 951 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.132923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.106556 restraints weight = 26883.344| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.62 r_work: 0.2819 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25080 Z= 0.176 Angle : 0.613 11.058 34133 Z= 0.325 Chirality : 0.047 0.314 3934 Planarity : 0.005 0.066 4358 Dihedral : 7.778 114.358 3893 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.56 % Allowed : 21.61 % Favored : 75.84 % 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 aren not related in a simple way. whole: -1.15 (0.14), residues: 3024 helix: 0.97 (0.20), residues: 699 sheet: 0.31 (0.19), residues: 705 loop : -2.16 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.024 0.002 TYR B 901 PHE 0.016 0.002 PHE C 830 TRP 0.011 0.001 TRP C 436 HIS 0.013 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00423 (25030) covalent geometry : angle 0.60050 (34016) SS BOND : bond 0.00453 ( 33) SS BOND : angle 1.48644 ( 66) hydrogen bonds : bond 0.06649 ( 947) hydrogen bonds : angle 5.19503 ( 2571) link_BETA1-4 : bond 0.00172 ( 3) link_BETA1-4 : angle 1.25197 ( 9) link_NAG-ASN : bond 0.00723 ( 14) link_NAG-ASN : angle 3.08757 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 229 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.8199 (t-90) cc_final: 0.7097 (m90) REVERT: C 357 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7665 (ttm170) REVERT: C 465 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: C 613 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: C 801 GLN cc_start: 0.8699 (mt0) cc_final: 0.8252 (mm110) REVERT: C 999 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8674 (tm-30) REVERT: C 1110 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8079 (mm110) REVERT: B 207 HIS cc_start: 0.7956 (t-90) cc_final: 0.7109 (m90) REVERT: B 239 GLN cc_start: 0.8906 (tt0) cc_final: 0.8608 (tt0) REVERT: B 244 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.5510 (pp) REVERT: B 321 GLN cc_start: 0.8585 (mm110) cc_final: 0.8281 (mm-40) REVERT: B 357 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.7655 (ttm170) REVERT: B 458 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8485 (mttp) REVERT: B 730 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8172 (mtmt) REVERT: B 801 GLN cc_start: 0.8726 (mt0) cc_final: 0.8278 (mm110) REVERT: B 947 ASP cc_start: 0.8379 (m-30) cc_final: 0.7961 (m-30) REVERT: B 1007 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8656 (mt0) REVERT: B 1047 MET cc_start: 0.9076 (ptm) cc_final: 0.8823 (ptm) REVERT: B 1110 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8207 (mm-40) REVERT: A 200 TYR cc_start: 0.8929 (m-80) cc_final: 0.8689 (m-80) REVERT: A 207 HIS cc_start: 0.8076 (t-90) cc_final: 0.7118 (m90) REVERT: A 244 LEU cc_start: 0.6060 (OUTLIER) cc_final: 0.5702 (pp) REVERT: A 554 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8267 (mm-30) REVERT: A 567 ARG cc_start: 0.8760 (mmt90) cc_final: 0.8548 (mmt90) REVERT: A 613 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: A 875 LEU cc_start: 0.9084 (mm) cc_final: 0.8725 (mt) REVERT: A 947 ASP cc_start: 0.8283 (m-30) cc_final: 0.7790 (m-30) REVERT: A 1110 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8232 (mm110) outliers start: 68 outliers final: 45 residues processed: 281 average time/residue: 0.5665 time to fit residues: 185.4739 Evaluate side-chains 285 residues out of total 2691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 225 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 9 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 291 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 44 optimal weight: 0.0670 chunk 247 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 185 optimal weight: 0.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN C1007 GLN B 603 ASN B1098 HIS A 951 GLN A1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.134274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.107875 restraints weight = 27022.501| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.70 r_work: 0.2844 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25080 Z= 0.133 Angle : 0.561 11.148 34133 Z= 0.298 Chirality : 0.045 0.305 3934 Planarity : 0.005 0.064 4358 Dihedral : 7.610 112.631 3893 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.37 % Allowed : 21.76 % Favored : 75.87 % 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 aren not related in a simple way. whole: -1.06 (0.14), residues: 3024 helix: 1.13 (0.20), residues: 696 sheet: 0.32 (0.19), residues: 705 loop : -2.12 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.015 0.001 TYR B 901 PHE 0.017 0.001 PHE C 830 TRP 0.011 0.001 TRP C 436 HIS 0.012 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00304 (25030) covalent geometry : angle 0.54846 (34016) SS BOND : bond 0.00324 ( 33) SS BOND : angle 1.23359 ( 66) hydrogen bonds : bond 0.05835 ( 947) hydrogen bonds : angle 5.10998 ( 2571) link_BETA1-4 : bond 0.00174 ( 3) link_BETA1-4 : angle 1.11003 ( 9) link_NAG-ASN : bond 0.00663 ( 14) link_NAG-ASN : angle 3.05220 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8121.34 seconds wall clock time: 139 minutes 7.08 seconds (8347.08 seconds total)