Starting phenix.real_space_refine on Sun Jul 5 22:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.map" model { file = "/net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ndc_12283/07_2026/7ndc_12283.cif" } resolution = 4.1 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= 0.002 sd= 0.021 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 135 5.16 5 C 19449 2.51 5 N 5079 2.21 5 O 5982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30645 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 8314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8314 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 856 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 793 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.27, per 1000 atoms: 0.24 Number of scatterers: 30645 At special positions: 0 Unit cell: (168.92, 183.68, 188.6, 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 135 16.00 O 5982 8.00 N 5079 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 165 " " NAG I 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.3 seconds 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7158 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 60 sheets defined 22.6% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.783A pdb=" N LEU A 368 " --> 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: 4.409A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.634A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.656A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.131A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.782A pdb=" N LEU B 368 " --> 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: 4.409A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.634A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.657A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.130A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.892A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.782A pdb=" N LEU C 368 " --> 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: 4.409A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.635A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.656A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.130A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.891A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.959A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.594A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 29 through 32 removed outlier: 3.993A pdb=" N ASN E 32 " --> pdb=" O ILE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 29 through 32' Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.593A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 29 through 32 removed outlier: 3.994A pdb=" N ASN G 32 " --> pdb=" O ILE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 29 through 32' Processing helix chain 'G' and resid 80 through 84 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.593A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 29 through 32 removed outlier: 3.993A pdb=" N ASN L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 29 through 32' Processing helix chain 'L' and resid 80 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.541A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.931A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.622A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.671A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.185A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.411A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.422A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.540A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.621A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.671A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.185A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.815A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.441A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.420A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.540A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.622A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL C 126 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.353A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.184A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.816A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.751A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.422A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY D 10 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 112 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.518A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AF4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY F 10 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL F 112 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.517A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.249A pdb=" N GLY H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL H 112 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.517A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 1265 hydrogen bonds defined for protein. 3381 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: 8.47 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9804 1.35 - 1.47: 7981 1.47 - 1.59: 13373 1.59 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 31332 Sorted by residual: bond pdb=" C1 NAG A1308 " pdb=" O5 NAG A1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.52e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.39e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.36e+00 ... (remaining 31327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 41122 1.34 - 2.69: 1207 2.69 - 4.03: 236 4.03 - 5.37: 20 5.37 - 6.71: 21 Bond angle restraints: 42606 Sorted by residual: angle pdb=" CA PRO A 527 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA PRO C 527 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 112.00 106.16 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA PRO B 527 " pdb=" N PRO B 527 " pdb=" CD PRO B 527 " ideal model delta sigma weight residual 112.00 106.20 5.80 1.40e+00 5.10e-01 1.71e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.28 -3.58 1.22e+00 6.72e-01 8.60e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.23 -3.53 1.22e+00 6.72e-01 8.35e+00 ... (remaining 42601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 17117 17.44 - 34.88: 807 34.88 - 52.31: 187 52.31 - 69.75: 51 69.75 - 87.19: 27 Dihedral angle restraints: 18189 sinusoidal: 7023 harmonic: 11166 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.19 79.19 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.19 79.19 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -165.16 79.16 1 1.00e+01 1.00e-02 7.79e+01 ... (remaining 18186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4004 0.054 - 0.108: 814 0.108 - 0.161: 108 0.161 - 0.215: 6 0.215 - 0.269: 3 Chirality restraints: 4935 Sorted by residual: chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 4932 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO A 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO B 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO C 527 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " 0.068 5.00e-02 4.00e+02 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 509 2.67 - 3.23: 28194 3.23 - 3.79: 46148 3.79 - 4.34: 63992 4.34 - 4.90: 106438 Nonbonded interactions: 245281 Sorted by model distance: nonbonded pdb=" NZ LYS B 147 " pdb=" OD1 ASN H 57 " model vdw 2.118 3.120 nonbonded pdb=" OE2 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR A 200 " pdb=" OE2 GLU C 516 " model vdw 2.195 3.040 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.237 3.040 ... (remaining 245276 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.360 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.003 0.086 31434 Z= 0.158 Angle : 0.569 6.713 42864 Z= 0.297 Chirality : 0.044 0.269 4935 Planarity : 0.005 0.127 5451 Dihedral : 11.704 87.188 10887 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.37 % Allowed : 4.02 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.13), residues: 3798 helix: 0.44 (0.18), residues: 744 sheet: 0.23 (0.15), residues: 1020 loop : -0.80 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 24 TYR 0.011 0.001 TYR L 37 PHE 0.009 0.001 PHE C 888 TRP 0.009 0.001 TRP C 258 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (31332) covalent geometry : angle 0.55955 / 0.30 (42606) SS BOND : bond 0.00250 / 0.17 ( 48) SS BOND : angle 1.03406 / 0.71 ( 96) hydrogen bonds : bond 0.18492 / 12.33 ( 1229) hydrogen bonds : angle 7.83445 / 5.39 ( 3381) link_BETA1-4 : bond 0.00217 / 0.13 ( 15) link_BETA1-4 : angle 0.80548 / 0.56 ( 45) link_NAG-ASN : bond 0.00179 / 0.09 ( 39) link_NAG-ASN : angle 1.87247 / 1.18 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 426 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8773 (p90) cc_final: 0.8380 (p90) REVERT: A 285 ILE cc_start: 0.8894 (mt) cc_final: 0.8635 (mt) REVERT: A 380 TYR cc_start: 0.8492 (m-80) cc_final: 0.7963 (m-80) REVERT: A 732 THR cc_start: 0.9242 (m) cc_final: 0.9026 (p) REVERT: A 736 VAL cc_start: 0.9222 (t) cc_final: 0.8799 (p) REVERT: A 740 MET cc_start: 0.8508 (ttt) cc_final: 0.8240 (ttm) REVERT: A 990 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8724 (pt0) REVERT: A 1023 ASN cc_start: 0.8816 (m-40) cc_final: 0.8497 (t0) REVERT: B 92 PHE cc_start: 0.8736 (t80) cc_final: 0.6941 (t80) REVERT: B 104 TRP cc_start: 0.7903 (m-90) cc_final: 0.7137 (m-90) REVERT: B 201 PHE cc_start: 0.8946 (t80) cc_final: 0.8267 (t80) REVERT: B 238 PHE cc_start: 0.8734 (p90) cc_final: 0.8457 (p90) REVERT: B 285 ILE cc_start: 0.8854 (mt) cc_final: 0.8555 (mt) REVERT: B 297 SER cc_start: 0.8481 (m) cc_final: 0.8130 (p) REVERT: B 380 TYR cc_start: 0.8442 (m-80) cc_final: 0.7893 (m-80) REVERT: B 402 ILE cc_start: 0.8493 (pt) cc_final: 0.8169 (pt) REVERT: B 610 VAL cc_start: 0.9528 (t) cc_final: 0.9282 (p) REVERT: B 724 THR cc_start: 0.9186 (m) cc_final: 0.8884 (p) REVERT: B 740 MET cc_start: 0.8478 (ttt) cc_final: 0.8267 (ttt) REVERT: B 990 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8493 (pt0) REVERT: B 994 ASP cc_start: 0.8984 (m-30) cc_final: 0.8636 (m-30) REVERT: C 92 PHE cc_start: 0.8560 (t80) cc_final: 0.7140 (t80) REVERT: C 104 TRP cc_start: 0.7968 (m-90) cc_final: 0.7264 (m-90) REVERT: C 285 ILE cc_start: 0.8943 (mt) cc_final: 0.8679 (mt) REVERT: C 297 SER cc_start: 0.8474 (m) cc_final: 0.8195 (p) REVERT: C 380 TYR cc_start: 0.8602 (m-80) cc_final: 0.8319 (m-80) REVERT: C 724 THR cc_start: 0.9326 (m) cc_final: 0.9009 (p) REVERT: C 732 THR cc_start: 0.9144 (m) cc_final: 0.8857 (p) REVERT: C 736 VAL cc_start: 0.9073 (t) cc_final: 0.8639 (p) REVERT: C 869 MET cc_start: 0.8600 (mtt) cc_final: 0.8142 (mtp) REVERT: C 870 ILE cc_start: 0.9473 (mm) cc_final: 0.9272 (pt) REVERT: C 884 SER cc_start: 0.8742 (p) cc_final: 0.8279 (m) REVERT: C 990 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8960 (pt0) REVERT: C 1023 ASN cc_start: 0.8664 (m-40) cc_final: 0.8360 (t0) REVERT: C 1029 MET cc_start: 0.9060 (tpp) cc_final: 0.8404 (tpp) outliers start: 12 outliers final: 0 residues processed: 438 average time/residue: 0.1975 time to fit residues: 140.6241 Evaluate side-chains 195 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 321 GLN A1005 GLN B 321 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 321 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.134259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083857 restraints weight = 110199.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.084039 restraints weight = 70904.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.085097 restraints weight = 44674.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.085585 restraints weight = 33073.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085735 restraints weight = 30189.700| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 31434 Z= 0.224 Angle : 0.657 16.112 42864 Z= 0.339 Chirality : 0.045 0.261 4935 Planarity : 0.005 0.155 5451 Dihedral : 4.496 24.573 4155 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.15 % Allowed : 1.92 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 3798 helix: 1.14 (0.20), residues: 732 sheet: 0.32 (0.15), residues: 996 loop : -0.44 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 357 TYR 0.033 0.002 TYR B 200 PHE 0.021 0.002 PHE B 377 TRP 0.024 0.001 TRP B 64 HIS 0.010 0.002 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (31332) covalent geometry : angle 0.64364 / 0.34 (42606) SS BOND : bond 0.01149 / 0.82 ( 48) SS BOND : angle 1.77141 / 1.17 ( 96) hydrogen bonds : bond 0.04927 / 3.30 ( 1229) hydrogen bonds : angle 6.24612 / 4.30 ( 3381) link_BETA1-4 : bond 0.00304 / 0.18 ( 15) link_BETA1-4 : angle 0.96084 / 0.68 ( 45) link_NAG-ASN : bond 0.00390 / 0.23 ( 39) link_NAG-ASN : angle 2.07156 / 1.30 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 249 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8878 (p90) cc_final: 0.8593 (p90) REVERT: A 369 TYR cc_start: 0.8673 (t80) cc_final: 0.8392 (t80) REVERT: A 380 TYR cc_start: 0.8828 (m-80) cc_final: 0.8235 (m-80) REVERT: A 732 THR cc_start: 0.9227 (m) cc_final: 0.8905 (p) REVERT: A 900 MET cc_start: 0.8960 (mmm) cc_final: 0.8748 (mmt) REVERT: A 902 MET cc_start: 0.9393 (mmm) cc_final: 0.8927 (tpp) REVERT: A 936 ASP cc_start: 0.9012 (t0) cc_final: 0.8716 (t0) REVERT: A 968 SER cc_start: 0.9487 (m) cc_final: 0.9158 (p) REVERT: A 990 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9036 (pt0) REVERT: B 92 PHE cc_start: 0.8782 (t80) cc_final: 0.8518 (t80) REVERT: B 238 PHE cc_start: 0.9009 (p90) cc_final: 0.8529 (p90) REVERT: B 297 SER cc_start: 0.8732 (m) cc_final: 0.8316 (p) REVERT: B 380 TYR cc_start: 0.8915 (m-80) cc_final: 0.8138 (m-80) REVERT: B 402 ILE cc_start: 0.8637 (pt) cc_final: 0.8343 (pt) REVERT: B 610 VAL cc_start: 0.9637 (t) cc_final: 0.9352 (p) REVERT: B 731 MET cc_start: 0.8864 (ptm) cc_final: 0.8609 (ptp) REVERT: B 737 ASP cc_start: 0.8656 (t70) cc_final: 0.7930 (p0) REVERT: B 740 MET cc_start: 0.8593 (ttt) cc_final: 0.7494 (ttt) REVERT: B 869 MET cc_start: 0.8721 (mtm) cc_final: 0.8269 (mtp) REVERT: B 936 ASP cc_start: 0.8853 (t0) cc_final: 0.8567 (t0) REVERT: B 990 GLU cc_start: 0.9214 (mt-10) cc_final: 0.9004 (pt0) REVERT: C 92 PHE cc_start: 0.9034 (t80) cc_final: 0.8584 (t80) REVERT: C 104 TRP cc_start: 0.8554 (m-90) cc_final: 0.8227 (m-90) REVERT: C 238 PHE cc_start: 0.8934 (p90) cc_final: 0.8328 (p90) REVERT: C 297 SER cc_start: 0.8855 (m) cc_final: 0.8449 (p) REVERT: C 380 TYR cc_start: 0.8937 (m-80) cc_final: 0.8641 (m-80) REVERT: C 387 LEU cc_start: 0.9390 (mt) cc_final: 0.9098 (mt) REVERT: C 402 ILE cc_start: 0.8601 (pt) cc_final: 0.8370 (pt) REVERT: C 731 MET cc_start: 0.9101 (ptm) cc_final: 0.8836 (ptp) REVERT: C 732 THR cc_start: 0.8811 (m) cc_final: 0.8564 (p) REVERT: C 740 MET cc_start: 0.8598 (ttt) cc_final: 0.8390 (ttt) REVERT: C 764 ASN cc_start: 0.8935 (t0) cc_final: 0.8497 (t0) REVERT: C 773 GLU cc_start: 0.8639 (tt0) cc_final: 0.7708 (tm-30) REVERT: C 869 MET cc_start: 0.8926 (mtt) cc_final: 0.8290 (mtp) REVERT: C 870 ILE cc_start: 0.9471 (mm) cc_final: 0.9268 (mt) REVERT: C 884 SER cc_start: 0.8793 (p) cc_final: 0.8507 (m) REVERT: C 900 MET cc_start: 0.8465 (tpp) cc_final: 0.8206 (tpp) REVERT: C 936 ASP cc_start: 0.8898 (t0) cc_final: 0.8661 (t0) REVERT: C 1029 MET cc_start: 0.9005 (tpp) cc_final: 0.7953 (tpp) REVERT: C 1050 MET cc_start: 0.8799 (ptp) cc_final: 0.8467 (ptm) REVERT: D 110 MET cc_start: 0.5331 (mmp) cc_final: 0.4548 (mmp) REVERT: F 110 MET cc_start: 0.5624 (mmp) cc_final: 0.4705 (mmp) REVERT: H 110 MET cc_start: 0.5834 (mmp) cc_final: 0.5120 (mmp) outliers start: 5 outliers final: 1 residues processed: 254 average time/residue: 0.1763 time to fit residues: 75.1415 Evaluate side-chains 179 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 213 optimal weight: 0.5980 chunk 190 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 225 optimal weight: 0.4980 chunk 278 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN A 955 ASN A1005 GLN B1005 GLN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.134808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085733 restraints weight = 109681.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086062 restraints weight = 69210.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086698 restraints weight = 38906.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087172 restraints weight = 34639.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087312 restraints weight = 30499.403| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31434 Z= 0.121 Angle : 0.545 15.680 42864 Z= 0.282 Chirality : 0.043 0.263 4935 Planarity : 0.004 0.039 5451 Dihedral : 4.153 19.824 4155 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.09 % Allowed : 1.28 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 3798 helix: 1.61 (0.20), residues: 702 sheet: 0.43 (0.15), residues: 1008 loop : -0.37 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 273 TYR 0.014 0.001 TYR A 904 PHE 0.020 0.001 PHE A 135 TRP 0.019 0.001 TRP A 104 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (31332) covalent geometry : angle 0.53384 / 0.28 (42606) SS BOND : bond 0.00341 / 0.23 ( 48) SS BOND : angle 1.71378 / 1.13 ( 96) hydrogen bonds : bond 0.04019 / 2.67 ( 1229) hydrogen bonds : angle 5.68012 / 3.92 ( 3381) link_BETA1-4 : bond 0.00362 / 0.22 ( 15) link_BETA1-4 : angle 0.90144 / 0.63 ( 45) link_NAG-ASN : bond 0.00268 / 0.16 ( 39) link_NAG-ASN : angle 1.46805 / 0.92 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7854 (m-10) cc_final: 0.7535 (m-10) REVERT: A 388 ASN cc_start: 0.7991 (p0) cc_final: 0.7288 (m-40) REVERT: A 773 GLU cc_start: 0.8178 (tt0) cc_final: 0.7789 (tm-30) REVERT: A 802 PHE cc_start: 0.8704 (m-80) cc_final: 0.8458 (m-10) REVERT: A 936 ASP cc_start: 0.8981 (t0) cc_final: 0.8636 (t0) REVERT: A 968 SER cc_start: 0.9437 (m) cc_final: 0.9127 (p) REVERT: A 984 LEU cc_start: 0.8586 (mm) cc_final: 0.7870 (tp) REVERT: A 990 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8995 (pt0) REVERT: B 92 PHE cc_start: 0.8571 (t80) cc_final: 0.7125 (t80) REVERT: B 104 TRP cc_start: 0.8322 (m-90) cc_final: 0.7561 (m-10) REVERT: B 238 PHE cc_start: 0.8983 (p90) cc_final: 0.8683 (p90) REVERT: B 297 SER cc_start: 0.8687 (m) cc_final: 0.8260 (p) REVERT: B 380 TYR cc_start: 0.8969 (m-80) cc_final: 0.8543 (m-80) REVERT: B 388 ASN cc_start: 0.7768 (p0) cc_final: 0.7187 (m-40) REVERT: B 610 VAL cc_start: 0.9621 (t) cc_final: 0.9324 (p) REVERT: B 731 MET cc_start: 0.8747 (ptm) cc_final: 0.8435 (ptp) REVERT: B 737 ASP cc_start: 0.8635 (t70) cc_final: 0.7917 (p0) REVERT: B 740 MET cc_start: 0.8677 (ttt) cc_final: 0.7472 (ttt) REVERT: B 773 GLU cc_start: 0.8538 (tt0) cc_final: 0.5344 (tm-30) REVERT: B 869 MET cc_start: 0.8691 (mtm) cc_final: 0.8254 (mtp) REVERT: B 936 ASP cc_start: 0.8852 (t0) cc_final: 0.8649 (t0) REVERT: B 990 GLU cc_start: 0.9203 (mt-10) cc_final: 0.9000 (pt0) REVERT: C 92 PHE cc_start: 0.8929 (t80) cc_final: 0.8468 (t80) REVERT: C 104 TRP cc_start: 0.8212 (m-90) cc_final: 0.7642 (m-90) REVERT: C 238 PHE cc_start: 0.8849 (p90) cc_final: 0.8528 (p90) REVERT: C 297 SER cc_start: 0.8773 (m) cc_final: 0.8372 (p) REVERT: C 387 LEU cc_start: 0.9361 (mt) cc_final: 0.8953 (mt) REVERT: C 388 ASN cc_start: 0.8549 (p0) cc_final: 0.8117 (m-40) REVERT: C 402 ILE cc_start: 0.8619 (pt) cc_final: 0.8364 (pt) REVERT: C 414 GLN cc_start: 0.8677 (mm-40) cc_final: 0.7972 (tm-30) REVERT: C 731 MET cc_start: 0.9030 (ptm) cc_final: 0.8711 (ptp) REVERT: C 732 THR cc_start: 0.8920 (m) cc_final: 0.8635 (p) REVERT: C 764 ASN cc_start: 0.8940 (t0) cc_final: 0.8487 (t0) REVERT: C 869 MET cc_start: 0.8852 (mtt) cc_final: 0.8338 (mtp) REVERT: C 884 SER cc_start: 0.8693 (p) cc_final: 0.8388 (m) REVERT: C 936 ASP cc_start: 0.8832 (t0) cc_final: 0.8597 (t0) REVERT: C 1029 MET cc_start: 0.9011 (tpp) cc_final: 0.7987 (tpp) REVERT: D 110 MET cc_start: 0.5288 (mmp) cc_final: 0.4356 (mmp) REVERT: F 110 MET cc_start: 0.5903 (mmp) cc_final: 0.4935 (mmp) REVERT: H 110 MET cc_start: 0.5555 (mmp) cc_final: 0.4825 (mmp) outliers start: 3 outliers final: 0 residues processed: 231 average time/residue: 0.1836 time to fit residues: 70.1504 Evaluate side-chains 159 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 370 optimal weight: 50.0000 chunk 252 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 316 optimal weight: 0.0980 chunk 106 optimal weight: 30.0000 chunk 101 optimal weight: 0.2980 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 239 GLN A1005 GLN B 901 GLN C 239 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.133113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082446 restraints weight = 108696.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.082939 restraints weight = 72674.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.082729 restraints weight = 45072.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.082930 restraints weight = 45885.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083169 restraints weight = 38916.211| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31434 Z= 0.163 Angle : 0.560 12.821 42864 Z= 0.289 Chirality : 0.043 0.327 4935 Planarity : 0.004 0.045 5451 Dihedral : 4.166 19.893 4155 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.09 % Allowed : 1.55 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3798 helix: 1.44 (0.20), residues: 702 sheet: 0.47 (0.15), residues: 1023 loop : -0.29 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1019 TYR 0.018 0.001 TYR A1067 PHE 0.033 0.002 PHE C 135 TRP 0.009 0.001 TRP F 36 HIS 0.006 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (31332) covalent geometry : angle 0.54934 / 0.29 (42606) SS BOND : bond 0.00414 / 0.30 ( 48) SS BOND : angle 1.75573 / 1.14 ( 96) hydrogen bonds : bond 0.04050 / 2.68 ( 1229) hydrogen bonds : angle 5.55365 / 3.83 ( 3381) link_BETA1-4 : bond 0.00257 / 0.16 ( 15) link_BETA1-4 : angle 0.97260 / 0.67 ( 45) link_NAG-ASN : bond 0.00269 / 0.16 ( 39) link_NAG-ASN : angle 1.42166 / 0.92 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8292 (m-90) cc_final: 0.7896 (m-10) REVERT: A 153 MET cc_start: 0.7883 (ptp) cc_final: 0.7650 (ppp) REVERT: A 238 PHE cc_start: 0.8884 (p90) cc_final: 0.8615 (p90) REVERT: A 388 ASN cc_start: 0.8096 (p0) cc_final: 0.7296 (m-40) REVERT: A 773 GLU cc_start: 0.8164 (tt0) cc_final: 0.7645 (tm-30) REVERT: A 936 ASP cc_start: 0.8986 (t0) cc_final: 0.8640 (t0) REVERT: A 968 SER cc_start: 0.9413 (m) cc_final: 0.9070 (p) REVERT: A 990 GLU cc_start: 0.9383 (mt-10) cc_final: 0.9009 (pt0) REVERT: B 92 PHE cc_start: 0.8837 (t80) cc_final: 0.7460 (t80) REVERT: B 104 TRP cc_start: 0.8691 (m-90) cc_final: 0.7697 (m-90) REVERT: B 153 MET cc_start: 0.7532 (ptp) cc_final: 0.7051 (ptm) REVERT: B 238 PHE cc_start: 0.9183 (p90) cc_final: 0.8814 (p90) REVERT: B 297 SER cc_start: 0.8724 (m) cc_final: 0.8354 (p) REVERT: B 387 LEU cc_start: 0.9337 (mt) cc_final: 0.8847 (mt) REVERT: B 388 ASN cc_start: 0.7995 (p0) cc_final: 0.7145 (m-40) REVERT: B 392 PHE cc_start: 0.8855 (m-80) cc_final: 0.8137 (m-80) REVERT: B 402 ILE cc_start: 0.8340 (pt) cc_final: 0.8091 (pt) REVERT: B 610 VAL cc_start: 0.9613 (t) cc_final: 0.9350 (p) REVERT: B 731 MET cc_start: 0.8751 (ptm) cc_final: 0.8482 (ptp) REVERT: B 737 ASP cc_start: 0.8595 (t70) cc_final: 0.7957 (p0) REVERT: B 740 MET cc_start: 0.8567 (ttt) cc_final: 0.7361 (ttt) REVERT: B 773 GLU cc_start: 0.8200 (tt0) cc_final: 0.7860 (tm-30) REVERT: B 869 MET cc_start: 0.8812 (mtm) cc_final: 0.8501 (mtp) REVERT: B 936 ASP cc_start: 0.8999 (t0) cc_final: 0.8715 (t0) REVERT: B 990 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8992 (pt0) REVERT: C 104 TRP cc_start: 0.8433 (m-90) cc_final: 0.7187 (m-10) REVERT: C 238 PHE cc_start: 0.9004 (p90) cc_final: 0.8651 (p90) REVERT: C 297 SER cc_start: 0.8851 (m) cc_final: 0.8418 (p) REVERT: C 387 LEU cc_start: 0.9387 (mt) cc_final: 0.8972 (mt) REVERT: C 388 ASN cc_start: 0.8772 (p0) cc_final: 0.8326 (m-40) REVERT: C 402 ILE cc_start: 0.8570 (pt) cc_final: 0.8311 (pt) REVERT: C 414 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8012 (tm-30) REVERT: C 731 MET cc_start: 0.9047 (ptm) cc_final: 0.8683 (ptp) REVERT: C 732 THR cc_start: 0.8935 (m) cc_final: 0.8672 (p) REVERT: C 764 ASN cc_start: 0.9046 (t0) cc_final: 0.8635 (t0) REVERT: C 869 MET cc_start: 0.8901 (mtt) cc_final: 0.8468 (mtp) REVERT: C 1029 MET cc_start: 0.8887 (tpp) cc_final: 0.7809 (tpp) REVERT: D 83 MET cc_start: -0.7019 (mmt) cc_final: -0.8185 (mtt) REVERT: D 110 MET cc_start: 0.5694 (mmp) cc_final: 0.4936 (mmp) REVERT: F 83 MET cc_start: -0.6788 (mmt) cc_final: -0.8002 (mtt) REVERT: F 110 MET cc_start: 0.5986 (mmp) cc_final: 0.5011 (mmp) REVERT: H 110 MET cc_start: 0.5669 (mmp) cc_final: 0.4856 (mmp) outliers start: 3 outliers final: 0 residues processed: 215 average time/residue: 0.1764 time to fit residues: 64.3636 Evaluate side-chains 157 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 326 optimal weight: 50.0000 chunk 155 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 367 optimal weight: 5.9990 chunk 317 optimal weight: 4.9990 chunk 362 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 655 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1119 ASN B 239 GLN B 655 HIS B1010 GLN B1119 ASN C 613 GLN C 655 HIS C1119 ASN D 35 HIS E 90 GLN F 35 HIS L 90 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.131707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.081157 restraints weight = 109973.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.079868 restraints weight = 70873.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080351 restraints weight = 49014.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080651 restraints weight = 44721.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080680 restraints weight = 40526.078| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31434 Z= 0.212 Angle : 0.592 13.154 42864 Z= 0.304 Chirality : 0.044 0.271 4935 Planarity : 0.004 0.060 5451 Dihedral : 4.241 19.105 4155 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.06 % Allowed : 1.55 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3798 helix: 1.20 (0.20), residues: 702 sheet: 0.38 (0.16), residues: 1008 loop : -0.28 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1039 TYR 0.025 0.001 TYR A1067 PHE 0.021 0.002 PHE A 906 TRP 0.008 0.001 TRP C 104 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (31332) covalent geometry : angle 0.58015 / 0.30 (42606) SS BOND : bond 0.00487 / 0.32 ( 48) SS BOND : angle 1.59126 / 1.01 ( 96) hydrogen bonds : bond 0.04177 / 2.77 ( 1229) hydrogen bonds : angle 5.59001 / 3.86 ( 3381) link_BETA1-4 : bond 0.00276 / 0.17 ( 15) link_BETA1-4 : angle 1.04296 / 0.72 ( 45) link_NAG-ASN : bond 0.00383 / 0.24 ( 39) link_NAG-ASN : angle 1.82929 / 1.17 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8144 (m-90) cc_final: 0.7713 (m-10) REVERT: A 153 MET cc_start: 0.7587 (ptp) cc_final: 0.7225 (ptm) REVERT: A 201 PHE cc_start: 0.9136 (t80) cc_final: 0.8671 (t80) REVERT: A 238 PHE cc_start: 0.8932 (p90) cc_final: 0.8658 (p90) REVERT: A 388 ASN cc_start: 0.8020 (p0) cc_final: 0.7365 (m-40) REVERT: A 773 GLU cc_start: 0.8242 (tt0) cc_final: 0.7715 (tm-30) REVERT: A 902 MET cc_start: 0.9402 (mmm) cc_final: 0.9085 (tpp) REVERT: A 936 ASP cc_start: 0.8996 (t0) cc_final: 0.8710 (t0) REVERT: A 968 SER cc_start: 0.9421 (m) cc_final: 0.9075 (p) REVERT: A 990 GLU cc_start: 0.9371 (mt-10) cc_final: 0.8992 (pt0) REVERT: B 60 SER cc_start: 0.8904 (t) cc_final: 0.8583 (p) REVERT: B 104 TRP cc_start: 0.8546 (m-90) cc_final: 0.7645 (m-10) REVERT: B 153 MET cc_start: 0.6837 (ptp) cc_final: 0.6523 (ptm) REVERT: B 238 PHE cc_start: 0.9198 (p90) cc_final: 0.8876 (p90) REVERT: B 297 SER cc_start: 0.8823 (m) cc_final: 0.8416 (p) REVERT: B 387 LEU cc_start: 0.9246 (mt) cc_final: 0.8902 (mt) REVERT: B 388 ASN cc_start: 0.7972 (p0) cc_final: 0.7324 (m-40) REVERT: B 392 PHE cc_start: 0.8899 (m-80) cc_final: 0.8184 (m-80) REVERT: B 402 ILE cc_start: 0.8553 (pt) cc_final: 0.8311 (pt) REVERT: B 414 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8311 (tm-30) REVERT: B 610 VAL cc_start: 0.9605 (t) cc_final: 0.9388 (p) REVERT: B 731 MET cc_start: 0.8805 (ptm) cc_final: 0.8455 (ptp) REVERT: B 737 ASP cc_start: 0.8533 (t70) cc_final: 0.7945 (p0) REVERT: B 740 MET cc_start: 0.8388 (ttt) cc_final: 0.7294 (ttt) REVERT: B 773 GLU cc_start: 0.8255 (tt0) cc_final: 0.7942 (tm-30) REVERT: B 869 MET cc_start: 0.8670 (mtm) cc_final: 0.8394 (mtp) REVERT: B 936 ASP cc_start: 0.8936 (t0) cc_final: 0.8651 (t0) REVERT: C 104 TRP cc_start: 0.8259 (m-90) cc_final: 0.7151 (m-10) REVERT: C 238 PHE cc_start: 0.9024 (p90) cc_final: 0.8816 (p90) REVERT: C 297 SER cc_start: 0.8896 (m) cc_final: 0.8436 (p) REVERT: C 387 LEU cc_start: 0.9444 (mt) cc_final: 0.9073 (mt) REVERT: C 388 ASN cc_start: 0.8700 (p0) cc_final: 0.8333 (m-40) REVERT: C 402 ILE cc_start: 0.8682 (pt) cc_final: 0.8408 (pt) REVERT: C 414 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8098 (tm-30) REVERT: C 731 MET cc_start: 0.9051 (ptm) cc_final: 0.8664 (ptp) REVERT: C 869 MET cc_start: 0.9030 (mtt) cc_final: 0.8587 (mtp) REVERT: D 83 MET cc_start: -0.6735 (mmt) cc_final: -0.8241 (mtt) REVERT: D 110 MET cc_start: 0.5303 (mmp) cc_final: 0.4409 (mmp) REVERT: F 83 MET cc_start: -0.6394 (mmt) cc_final: -0.8143 (mtt) REVERT: F 110 MET cc_start: 0.5711 (mmp) cc_final: 0.4816 (mmp) REVERT: H 110 MET cc_start: 0.5663 (mmp) cc_final: 0.4826 (mmp) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.1715 time to fit residues: 57.9498 Evaluate side-chains 147 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 290 optimal weight: 0.6980 chunk 152 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 245 optimal weight: 7.9990 chunk 296 optimal weight: 0.5980 chunk 350 optimal weight: 8.9990 chunk 304 optimal weight: 0.5980 chunk 250 optimal weight: 0.4980 chunk 129 optimal weight: 20.0000 chunk 299 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 913 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.132599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083731 restraints weight = 109098.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.083160 restraints weight = 68857.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082983 restraints weight = 47715.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.083410 restraints weight = 46496.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.083455 restraints weight = 41491.581| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31434 Z= 0.124 Angle : 0.523 12.928 42864 Z= 0.271 Chirality : 0.042 0.260 4935 Planarity : 0.003 0.043 5451 Dihedral : 4.044 23.007 4155 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.03 % Allowed : 1.04 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3798 helix: 1.33 (0.20), residues: 702 sheet: 0.49 (0.16), residues: 1017 loop : -0.25 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1039 TYR 0.012 0.001 TYR C1067 PHE 0.018 0.001 PHE C 906 TRP 0.009 0.001 TRP B 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (31332) covalent geometry : angle 0.51409 / 0.27 (42606) SS BOND : bond 0.00591 / 0.39 ( 48) SS BOND : angle 1.54906 / 1.01 ( 96) hydrogen bonds : bond 0.03821 / 2.54 ( 1229) hydrogen bonds : angle 5.32713 / 3.68 ( 3381) link_BETA1-4 : bond 0.00331 / 0.20 ( 15) link_BETA1-4 : angle 0.92671 / 0.64 ( 45) link_NAG-ASN : bond 0.00241 / 0.14 ( 39) link_NAG-ASN : angle 1.26334 / 0.81 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 200 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7961 (m-90) cc_final: 0.7642 (m-10) REVERT: A 153 MET cc_start: 0.7310 (ptp) cc_final: 0.6825 (ptm) REVERT: A 201 PHE cc_start: 0.9118 (t80) cc_final: 0.8609 (t80) REVERT: A 238 PHE cc_start: 0.8842 (p90) cc_final: 0.8541 (p90) REVERT: A 388 ASN cc_start: 0.7836 (p0) cc_final: 0.7112 (m-40) REVERT: A 902 MET cc_start: 0.9435 (mmm) cc_final: 0.9190 (mmt) REVERT: A 936 ASP cc_start: 0.9098 (t0) cc_final: 0.8712 (t0) REVERT: A 968 SER cc_start: 0.9459 (m) cc_final: 0.9115 (t) REVERT: A 990 GLU cc_start: 0.9368 (mt-10) cc_final: 0.8989 (pt0) REVERT: B 60 SER cc_start: 0.8797 (t) cc_final: 0.8552 (t) REVERT: B 92 PHE cc_start: 0.8769 (t80) cc_final: 0.7558 (t80) REVERT: B 104 TRP cc_start: 0.8445 (m-90) cc_final: 0.7398 (m-90) REVERT: B 238 PHE cc_start: 0.9159 (p90) cc_final: 0.8763 (p90) REVERT: B 297 SER cc_start: 0.8749 (m) cc_final: 0.8355 (p) REVERT: B 387 LEU cc_start: 0.9151 (mt) cc_final: 0.8855 (mt) REVERT: B 388 ASN cc_start: 0.7878 (p0) cc_final: 0.7169 (m-40) REVERT: B 392 PHE cc_start: 0.8817 (m-80) cc_final: 0.8089 (m-80) REVERT: B 402 ILE cc_start: 0.8509 (pt) cc_final: 0.8268 (pt) REVERT: B 414 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8367 (tm-30) REVERT: B 610 VAL cc_start: 0.9601 (t) cc_final: 0.9382 (p) REVERT: B 731 MET cc_start: 0.8727 (ptm) cc_final: 0.8336 (ptp) REVERT: B 737 ASP cc_start: 0.8445 (t70) cc_final: 0.7826 (p0) REVERT: B 740 MET cc_start: 0.8400 (ttt) cc_final: 0.7807 (ttt) REVERT: B 773 GLU cc_start: 0.8174 (tt0) cc_final: 0.7855 (tm-30) REVERT: B 869 MET cc_start: 0.8749 (mtm) cc_final: 0.8381 (mtp) REVERT: B 902 MET cc_start: 0.9628 (mmm) cc_final: 0.9230 (mmm) REVERT: B 936 ASP cc_start: 0.9012 (t0) cc_final: 0.8693 (t0) REVERT: B 990 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9044 (pt0) REVERT: C 104 TRP cc_start: 0.8207 (m-90) cc_final: 0.7102 (m-10) REVERT: C 297 SER cc_start: 0.8841 (m) cc_final: 0.8376 (p) REVERT: C 377 PHE cc_start: 0.8600 (t80) cc_final: 0.8379 (t80) REVERT: C 387 LEU cc_start: 0.9385 (mt) cc_final: 0.9052 (mt) REVERT: C 388 ASN cc_start: 0.8610 (p0) cc_final: 0.8163 (m-40) REVERT: C 402 ILE cc_start: 0.8576 (pt) cc_final: 0.8302 (pt) REVERT: C 414 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8144 (tm-30) REVERT: C 731 MET cc_start: 0.8947 (ptm) cc_final: 0.8597 (ptp) REVERT: C 764 ASN cc_start: 0.8978 (t0) cc_final: 0.8545 (t0) REVERT: C 869 MET cc_start: 0.8838 (mtt) cc_final: 0.8568 (mtp) REVERT: C 1029 MET cc_start: 0.9066 (tpp) cc_final: 0.7863 (tpp) REVERT: D 83 MET cc_start: -0.6717 (mmt) cc_final: -0.8226 (mtt) REVERT: D 110 MET cc_start: 0.5097 (mmp) cc_final: 0.4017 (mmp) REVERT: F 83 MET cc_start: -0.6345 (mmt) cc_final: -0.8033 (mtt) REVERT: F 110 MET cc_start: 0.5521 (mmp) cc_final: 0.4625 (mmp) REVERT: H 110 MET cc_start: 0.5842 (mmp) cc_final: 0.5002 (mmp) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.1787 time to fit residues: 60.4689 Evaluate side-chains 146 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 18 optimal weight: 0.0170 chunk 162 optimal weight: 0.2980 chunk 292 optimal weight: 0.0670 chunk 194 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 336 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 179 optimal weight: 0.0050 chunk 337 optimal weight: 10.0000 overall best weight: 0.1970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 613 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.133839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.083129 restraints weight = 108959.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084174 restraints weight = 67797.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.084205 restraints weight = 38951.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084277 restraints weight = 40969.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.084974 restraints weight = 35640.762| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 31434 Z= 0.092 Angle : 0.502 12.561 42864 Z= 0.260 Chirality : 0.042 0.254 4935 Planarity : 0.003 0.044 5451 Dihedral : 3.850 17.860 4155 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.03 % Allowed : 0.82 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.14), residues: 3798 helix: 1.60 (0.21), residues: 696 sheet: 0.77 (0.16), residues: 1005 loop : -0.25 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 995 TYR 0.014 0.001 TYR B 904 PHE 0.017 0.001 PHE A 464 TRP 0.008 0.001 TRP B 152 HIS 0.007 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 (31332) covalent geometry : angle 0.49282 / 0.26 (42606) SS BOND : bond 0.00375 / 0.25 ( 48) SS BOND : angle 1.59663 / 1.09 ( 96) hydrogen bonds : bond 0.03536 / 2.34 ( 1229) hydrogen bonds : angle 5.09331 / 3.52 ( 3381) link_BETA1-4 : bond 0.00396 / 0.24 ( 15) link_BETA1-4 : angle 0.92302 / 0.63 ( 45) link_NAG-ASN : bond 0.00240 / 0.15 ( 39) link_NAG-ASN : angle 1.13235 / 0.72 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8160 (m-90) cc_final: 0.7773 (m-10) REVERT: A 153 MET cc_start: 0.7410 (ptp) cc_final: 0.7028 (ppp) REVERT: A 201 PHE cc_start: 0.8996 (t80) cc_final: 0.8651 (t80) REVERT: A 238 PHE cc_start: 0.8908 (p90) cc_final: 0.8588 (p90) REVERT: A 387 LEU cc_start: 0.9494 (mt) cc_final: 0.9097 (mt) REVERT: A 388 ASN cc_start: 0.7901 (p0) cc_final: 0.7074 (m-40) REVERT: A 425 LEU cc_start: 0.9075 (tt) cc_final: 0.8841 (tt) REVERT: A 936 ASP cc_start: 0.9002 (t0) cc_final: 0.8584 (t0) REVERT: A 968 SER cc_start: 0.9381 (m) cc_final: 0.9005 (t) REVERT: A 984 LEU cc_start: 0.8613 (mm) cc_final: 0.8154 (tp) REVERT: A 990 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8981 (pt0) REVERT: B 60 SER cc_start: 0.8720 (t) cc_final: 0.8505 (t) REVERT: B 92 PHE cc_start: 0.8921 (t80) cc_final: 0.7652 (t80) REVERT: B 104 TRP cc_start: 0.8521 (m-90) cc_final: 0.7327 (m-90) REVERT: B 118 LEU cc_start: 0.9415 (tt) cc_final: 0.9035 (mt) REVERT: B 135 PHE cc_start: 0.8701 (m-10) cc_final: 0.8307 (m-10) REVERT: B 153 MET cc_start: 0.7290 (ppp) cc_final: 0.6937 (ppp) REVERT: B 238 PHE cc_start: 0.9202 (p90) cc_final: 0.8758 (p90) REVERT: B 297 SER cc_start: 0.8580 (m) cc_final: 0.8158 (p) REVERT: B 378 LYS cc_start: 0.9561 (mptt) cc_final: 0.9337 (mmtt) REVERT: B 387 LEU cc_start: 0.9174 (mt) cc_final: 0.8734 (mt) REVERT: B 388 ASN cc_start: 0.7993 (p0) cc_final: 0.7167 (m-40) REVERT: B 392 PHE cc_start: 0.8834 (m-80) cc_final: 0.8095 (m-80) REVERT: B 402 ILE cc_start: 0.8602 (pt) cc_final: 0.8364 (pt) REVERT: B 610 VAL cc_start: 0.9573 (t) cc_final: 0.9358 (p) REVERT: B 731 MET cc_start: 0.8651 (ptm) cc_final: 0.8305 (ptp) REVERT: B 737 ASP cc_start: 0.8428 (t70) cc_final: 0.7781 (p0) REVERT: B 740 MET cc_start: 0.8581 (ttt) cc_final: 0.7962 (ttt) REVERT: B 773 GLU cc_start: 0.8228 (tt0) cc_final: 0.7739 (tm-30) REVERT: B 869 MET cc_start: 0.8581 (mtm) cc_final: 0.8286 (mtp) REVERT: B 902 MET cc_start: 0.9575 (mmm) cc_final: 0.9261 (mmm) REVERT: B 936 ASP cc_start: 0.9003 (t0) cc_final: 0.8702 (t0) REVERT: B 990 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9082 (pt0) REVERT: B 1001 LEU cc_start: 0.9443 (tp) cc_final: 0.9203 (tp) REVERT: C 92 PHE cc_start: 0.9072 (t80) cc_final: 0.8608 (t80) REVERT: C 104 TRP cc_start: 0.8319 (m-90) cc_final: 0.7908 (m-90) REVERT: C 238 PHE cc_start: 0.8983 (p90) cc_final: 0.8572 (p90) REVERT: C 297 SER cc_start: 0.8810 (m) cc_final: 0.8303 (p) REVERT: C 387 LEU cc_start: 0.9385 (mt) cc_final: 0.8944 (mt) REVERT: C 388 ASN cc_start: 0.8652 (p0) cc_final: 0.8179 (m-40) REVERT: C 402 ILE cc_start: 0.8564 (pt) cc_final: 0.8273 (pt) REVERT: C 414 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8282 (tm-30) REVERT: C 731 MET cc_start: 0.8920 (ptm) cc_final: 0.8562 (ptp) REVERT: C 869 MET cc_start: 0.8904 (mtt) cc_final: 0.8397 (mtp) REVERT: C 936 ASP cc_start: 0.8706 (t70) cc_final: 0.8467 (t0) REVERT: C 1029 MET cc_start: 0.9124 (tpp) cc_final: 0.7858 (tpp) REVERT: D 83 MET cc_start: -0.6584 (mmt) cc_final: -0.8161 (mtt) REVERT: D 110 MET cc_start: 0.5005 (mmp) cc_final: 0.3961 (mmp) REVERT: F 83 MET cc_start: -0.6209 (mmt) cc_final: -0.7846 (mtt) REVERT: F 110 MET cc_start: 0.5449 (mmp) cc_final: 0.4570 (mmp) REVERT: H 110 MET cc_start: 0.5844 (mmp) cc_final: 0.5004 (mmp) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1708 time to fit residues: 61.3062 Evaluate side-chains 150 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 59 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 338 optimal weight: 0.5980 chunk 252 optimal weight: 0.7980 chunk 225 optimal weight: 0.0870 chunk 277 optimal weight: 0.0570 chunk 251 optimal weight: 5.9990 chunk 323 optimal weight: 5.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 519 HIS C 207 HIS H 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.133628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086810 restraints weight = 109565.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085905 restraints weight = 66745.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084966 restraints weight = 51753.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085439 restraints weight = 53367.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086192 restraints weight = 43143.693| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 31434 Z= 0.094 Angle : 0.490 12.187 42864 Z= 0.255 Chirality : 0.042 0.221 4935 Planarity : 0.003 0.046 5451 Dihedral : 3.761 16.903 4155 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.03 % Allowed : 0.76 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3798 helix: 1.59 (0.21), residues: 702 sheet: 0.83 (0.16), residues: 1035 loop : -0.22 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 408 TYR 0.014 0.001 TYR B 904 PHE 0.018 0.001 PHE B 464 TRP 0.007 0.001 TRP F 36 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (31332) covalent geometry : angle 0.48203 / 0.25 (42606) SS BOND : bond 0.00430 / 0.28 ( 48) SS BOND : angle 1.40980 / 0.99 ( 96) hydrogen bonds : bond 0.03476 / 2.32 ( 1229) hydrogen bonds : angle 5.02702 / 3.49 ( 3381) link_BETA1-4 : bond 0.00320 / 0.19 ( 15) link_BETA1-4 : angle 0.95425 / 0.65 ( 45) link_NAG-ASN : bond 0.00183 / 0.11 ( 39) link_NAG-ASN : angle 1.11248 / 0.73 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7969 (m-90) cc_final: 0.7625 (m-10) REVERT: A 153 MET cc_start: 0.7279 (ptp) cc_final: 0.6907 (ppp) REVERT: A 201 PHE cc_start: 0.8991 (t80) cc_final: 0.8620 (t80) REVERT: A 238 PHE cc_start: 0.8864 (p90) cc_final: 0.8552 (p90) REVERT: A 387 LEU cc_start: 0.9457 (mt) cc_final: 0.9091 (mt) REVERT: A 388 ASN cc_start: 0.7885 (p0) cc_final: 0.7083 (m-40) REVERT: A 402 ILE cc_start: 0.8724 (pt) cc_final: 0.8517 (pt) REVERT: A 936 ASP cc_start: 0.9151 (t0) cc_final: 0.8728 (t0) REVERT: A 968 SER cc_start: 0.9351 (m) cc_final: 0.8969 (t) REVERT: A 984 LEU cc_start: 0.8606 (mm) cc_final: 0.8142 (tp) REVERT: A 990 GLU cc_start: 0.9374 (mt-10) cc_final: 0.8958 (pt0) REVERT: B 60 SER cc_start: 0.8719 (t) cc_final: 0.8510 (t) REVERT: B 92 PHE cc_start: 0.8800 (t80) cc_final: 0.7548 (t80) REVERT: B 104 TRP cc_start: 0.8436 (m-90) cc_final: 0.7265 (m-90) REVERT: B 118 LEU cc_start: 0.9380 (tt) cc_final: 0.9022 (mt) REVERT: B 135 PHE cc_start: 0.8688 (m-10) cc_final: 0.8322 (m-10) REVERT: B 238 PHE cc_start: 0.9161 (p90) cc_final: 0.8727 (p90) REVERT: B 297 SER cc_start: 0.8582 (m) cc_final: 0.8159 (p) REVERT: B 378 LYS cc_start: 0.9562 (mptt) cc_final: 0.9180 (mmtt) REVERT: B 387 LEU cc_start: 0.9172 (mt) cc_final: 0.8750 (mt) REVERT: B 388 ASN cc_start: 0.8007 (p0) cc_final: 0.7208 (m-40) REVERT: B 392 PHE cc_start: 0.8775 (m-80) cc_final: 0.7990 (m-80) REVERT: B 402 ILE cc_start: 0.8587 (pt) cc_final: 0.8325 (pt) REVERT: B 414 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8358 (tm-30) REVERT: B 610 VAL cc_start: 0.9545 (t) cc_final: 0.9331 (p) REVERT: B 731 MET cc_start: 0.8544 (ptm) cc_final: 0.8256 (ptp) REVERT: B 737 ASP cc_start: 0.8416 (t70) cc_final: 0.7765 (p0) REVERT: B 740 MET cc_start: 0.8615 (ttt) cc_final: 0.8039 (ttt) REVERT: B 773 GLU cc_start: 0.8110 (tt0) cc_final: 0.7755 (tm-30) REVERT: B 869 MET cc_start: 0.8649 (mtm) cc_final: 0.8259 (mtp) REVERT: B 902 MET cc_start: 0.9515 (mmm) cc_final: 0.9240 (mmm) REVERT: B 936 ASP cc_start: 0.9062 (t0) cc_final: 0.8766 (t0) REVERT: B 968 SER cc_start: 0.9060 (m) cc_final: 0.8718 (t) REVERT: B 990 GLU cc_start: 0.9339 (mt-10) cc_final: 0.9044 (pt0) REVERT: C 92 PHE cc_start: 0.8996 (t80) cc_final: 0.8535 (t80) REVERT: C 104 TRP cc_start: 0.8250 (m-90) cc_final: 0.7820 (m-90) REVERT: C 238 PHE cc_start: 0.8952 (p90) cc_final: 0.8580 (p90) REVERT: C 297 SER cc_start: 0.8835 (m) cc_final: 0.8305 (p) REVERT: C 388 ASN cc_start: 0.8775 (p0) cc_final: 0.8322 (m-40) REVERT: C 402 ILE cc_start: 0.8561 (pt) cc_final: 0.8274 (pt) REVERT: C 414 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8303 (tm-30) REVERT: C 731 MET cc_start: 0.8884 (ptm) cc_final: 0.8536 (ptp) REVERT: C 869 MET cc_start: 0.8924 (mtt) cc_final: 0.8434 (mtp) REVERT: C 936 ASP cc_start: 0.8798 (t70) cc_final: 0.8561 (t0) REVERT: D 83 MET cc_start: -0.6560 (mmt) cc_final: -0.8136 (mtt) REVERT: D 110 MET cc_start: 0.5198 (mmp) cc_final: 0.4154 (mmp) REVERT: F 83 MET cc_start: -0.6277 (mmt) cc_final: -0.7915 (mtt) REVERT: F 110 MET cc_start: 0.5579 (mmp) cc_final: 0.4761 (mmp) REVERT: H 110 MET cc_start: 0.5787 (mmp) cc_final: 0.4938 (mmp) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1694 time to fit residues: 60.1711 Evaluate side-chains 155 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 375 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 0.0970 chunk 239 optimal weight: 0.9990 chunk 212 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN A1005 GLN B 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.132251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081462 restraints weight = 109248.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.081863 restraints weight = 77032.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.081453 restraints weight = 48640.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081886 restraints weight = 49386.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.082378 restraints weight = 39684.936| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31434 Z= 0.159 Angle : 0.532 11.596 42864 Z= 0.275 Chirality : 0.042 0.225 4935 Planarity : 0.003 0.045 5451 Dihedral : 3.860 18.547 4155 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3798 helix: 1.43 (0.20), residues: 702 sheet: 0.68 (0.16), residues: 960 loop : -0.21 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 403 TYR 0.028 0.001 TYR B 904 PHE 0.020 0.001 PHE A 906 TRP 0.008 0.001 TRP D 36 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (31332) covalent geometry : angle 0.52381 / 0.27 (42606) SS BOND : bond 0.00491 / 0.32 ( 48) SS BOND : angle 1.45121 / 1.05 ( 96) hydrogen bonds : bond 0.03799 / 2.53 ( 1229) hydrogen bonds : angle 5.15216 / 3.57 ( 3381) link_BETA1-4 : bond 0.00233 / 0.14 ( 15) link_BETA1-4 : angle 1.02942 / 0.70 ( 45) link_NAG-ASN : bond 0.00211 / 0.13 ( 39) link_NAG-ASN : angle 1.20229 / 0.80 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8149 (m-90) cc_final: 0.7716 (m-10) REVERT: A 153 MET cc_start: 0.7403 (ptp) cc_final: 0.7001 (ppp) REVERT: A 201 PHE cc_start: 0.9238 (t80) cc_final: 0.8691 (t80) REVERT: A 238 PHE cc_start: 0.8972 (p90) cc_final: 0.8673 (p90) REVERT: A 387 LEU cc_start: 0.9535 (mt) cc_final: 0.9135 (mt) REVERT: A 388 ASN cc_start: 0.7945 (p0) cc_final: 0.7106 (m-40) REVERT: A 775 ASP cc_start: 0.8664 (m-30) cc_final: 0.8374 (m-30) REVERT: A 936 ASP cc_start: 0.9095 (t0) cc_final: 0.8673 (t0) REVERT: A 968 SER cc_start: 0.9388 (m) cc_final: 0.8990 (t) REVERT: A 990 GLU cc_start: 0.9383 (mt-10) cc_final: 0.8975 (pt0) REVERT: A 994 ASP cc_start: 0.8706 (m-30) cc_final: 0.8497 (m-30) REVERT: B 60 SER cc_start: 0.8753 (t) cc_final: 0.8539 (t) REVERT: B 92 PHE cc_start: 0.8875 (t80) cc_final: 0.7623 (t80) REVERT: B 104 TRP cc_start: 0.8549 (m-90) cc_final: 0.7368 (m-90) REVERT: B 118 LEU cc_start: 0.9422 (tt) cc_final: 0.9068 (mt) REVERT: B 135 PHE cc_start: 0.8684 (m-10) cc_final: 0.8395 (m-10) REVERT: B 153 MET cc_start: 0.7266 (ppp) cc_final: 0.6956 (ppp) REVERT: B 238 PHE cc_start: 0.9244 (p90) cc_final: 0.8839 (p90) REVERT: B 297 SER cc_start: 0.8625 (m) cc_final: 0.8185 (p) REVERT: B 387 LEU cc_start: 0.9226 (mt) cc_final: 0.8811 (mt) REVERT: B 388 ASN cc_start: 0.8108 (p0) cc_final: 0.7274 (m-40) REVERT: B 392 PHE cc_start: 0.8829 (m-80) cc_final: 0.8074 (m-80) REVERT: B 402 ILE cc_start: 0.8654 (pt) cc_final: 0.8389 (pt) REVERT: B 414 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8366 (tm-30) REVERT: B 731 MET cc_start: 0.8606 (ptm) cc_final: 0.8298 (ptp) REVERT: B 740 MET cc_start: 0.8508 (ttt) cc_final: 0.8204 (ttt) REVERT: B 773 GLU cc_start: 0.8154 (tt0) cc_final: 0.7818 (tm-30) REVERT: B 869 MET cc_start: 0.8830 (mtm) cc_final: 0.8383 (mtp) REVERT: B 902 MET cc_start: 0.9618 (mmm) cc_final: 0.9302 (mmm) REVERT: B 936 ASP cc_start: 0.9113 (t0) cc_final: 0.8816 (t0) REVERT: B 990 GLU cc_start: 0.9334 (mt-10) cc_final: 0.9054 (pt0) REVERT: C 104 TRP cc_start: 0.8387 (m-90) cc_final: 0.7281 (m-10) REVERT: C 238 PHE cc_start: 0.9081 (p90) cc_final: 0.8687 (p90) REVERT: C 297 SER cc_start: 0.8850 (m) cc_final: 0.8340 (p) REVERT: C 377 PHE cc_start: 0.8835 (t80) cc_final: 0.8579 (t80) REVERT: C 388 ASN cc_start: 0.8849 (p0) cc_final: 0.8370 (m-40) REVERT: C 402 ILE cc_start: 0.8610 (pt) cc_final: 0.8361 (pt) REVERT: C 414 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8312 (tm-30) REVERT: C 697 MET cc_start: 0.7994 (ptm) cc_final: 0.7738 (ttp) REVERT: C 731 MET cc_start: 0.8933 (ptm) cc_final: 0.8539 (ptp) REVERT: C 869 MET cc_start: 0.8955 (mtt) cc_final: 0.8525 (mtp) REVERT: C 936 ASP cc_start: 0.8797 (t70) cc_final: 0.8590 (t0) REVERT: D 83 MET cc_start: -0.6562 (mmt) cc_final: -0.8144 (mtt) REVERT: D 110 MET cc_start: 0.5407 (mmp) cc_final: 0.4409 (mmp) REVERT: F 83 MET cc_start: -0.6214 (mmt) cc_final: -0.7856 (mtt) REVERT: F 110 MET cc_start: 0.5106 (mmp) cc_final: 0.4324 (mmp) REVERT: H 110 MET cc_start: 0.5817 (mmp) cc_final: 0.4962 (mmp) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.1603 time to fit residues: 53.5992 Evaluate side-chains 145 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 141 optimal weight: 30.0000 chunk 96 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 363 optimal weight: 7.9990 chunk 298 optimal weight: 2.9990 chunk 314 optimal weight: 0.5980 chunk 288 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 320 optimal weight: 40.0000 chunk 79 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 913 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.133087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081235 restraints weight = 105045.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.080313 restraints weight = 70890.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.080521 restraints weight = 48360.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.080873 restraints weight = 47671.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080983 restraints weight = 38861.732| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 31434 Z= 0.168 Angle : 0.546 11.338 42864 Z= 0.283 Chirality : 0.043 0.217 4935 Planarity : 0.004 0.045 5451 Dihedral : 3.957 19.202 4155 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3798 helix: 1.28 (0.20), residues: 705 sheet: 0.63 (0.17), residues: 963 loop : -0.25 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.033 0.001 TYR B 904 PHE 0.022 0.001 PHE C 888 TRP 0.006 0.001 TRP B 886 HIS 0.010 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (31332) covalent geometry : angle 0.53878 / 0.28 (42606) SS BOND : bond 0.00422 / 0.28 ( 48) SS BOND : angle 1.36434 / 0.99 ( 96) hydrogen bonds : bond 0.03949 / 2.61 ( 1229) hydrogen bonds : angle 5.22669 / 3.63 ( 3381) link_BETA1-4 : bond 0.00268 / 0.17 ( 15) link_BETA1-4 : angle 1.02913 / 0.70 ( 45) link_NAG-ASN : bond 0.00234 / 0.15 ( 39) link_NAG-ASN : angle 1.23103 / 0.83 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7982 (m-90) cc_final: 0.7600 (m-10) REVERT: A 153 MET cc_start: 0.7305 (ptp) cc_final: 0.6907 (ppp) REVERT: A 201 PHE cc_start: 0.9131 (t80) cc_final: 0.8550 (t80) REVERT: A 238 PHE cc_start: 0.8816 (p90) cc_final: 0.8573 (p90) REVERT: A 377 PHE cc_start: 0.8833 (t80) cc_final: 0.8300 (t80) REVERT: A 387 LEU cc_start: 0.9511 (mt) cc_final: 0.8881 (mt) REVERT: A 936 ASP cc_start: 0.9095 (t0) cc_final: 0.8731 (t0) REVERT: A 968 SER cc_start: 0.9420 (m) cc_final: 0.9040 (t) REVERT: A 990 GLU cc_start: 0.9331 (mt-10) cc_final: 0.8926 (pt0) REVERT: B 60 SER cc_start: 0.8800 (t) cc_final: 0.8580 (t) REVERT: B 104 TRP cc_start: 0.8361 (m-90) cc_final: 0.7369 (m-10) REVERT: B 118 LEU cc_start: 0.9383 (tt) cc_final: 0.9017 (mt) REVERT: B 135 PHE cc_start: 0.8641 (m-10) cc_final: 0.8354 (m-10) REVERT: B 153 MET cc_start: 0.6786 (ppp) cc_final: 0.6479 (ppp) REVERT: B 238 PHE cc_start: 0.9175 (p90) cc_final: 0.8825 (p90) REVERT: B 297 SER cc_start: 0.8708 (m) cc_final: 0.8237 (p) REVERT: B 387 LEU cc_start: 0.9209 (mt) cc_final: 0.8827 (mt) REVERT: B 388 ASN cc_start: 0.8052 (p0) cc_final: 0.7414 (m-40) REVERT: B 392 PHE cc_start: 0.8793 (m-80) cc_final: 0.8057 (m-80) REVERT: B 402 ILE cc_start: 0.8827 (pt) cc_final: 0.8579 (pt) REVERT: B 414 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8408 (tm-30) REVERT: B 425 LEU cc_start: 0.9277 (tp) cc_final: 0.9066 (tp) REVERT: B 731 MET cc_start: 0.8579 (ptm) cc_final: 0.8302 (ptp) REVERT: B 740 MET cc_start: 0.8402 (ttt) cc_final: 0.8029 (ttt) REVERT: B 773 GLU cc_start: 0.8213 (tt0) cc_final: 0.7880 (tm-30) REVERT: B 869 MET cc_start: 0.8806 (mtm) cc_final: 0.8483 (mtp) REVERT: B 902 MET cc_start: 0.9618 (mmm) cc_final: 0.9343 (mmm) REVERT: B 936 ASP cc_start: 0.9098 (t0) cc_final: 0.8812 (t0) REVERT: B 990 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9041 (pt0) REVERT: B 1001 LEU cc_start: 0.9427 (tp) cc_final: 0.9168 (tp) REVERT: C 54 LEU cc_start: 0.9373 (mm) cc_final: 0.8958 (tp) REVERT: C 104 TRP cc_start: 0.8243 (m-90) cc_final: 0.7681 (m-90) REVERT: C 238 PHE cc_start: 0.9005 (p90) cc_final: 0.8648 (p90) REVERT: C 297 SER cc_start: 0.8841 (m) cc_final: 0.8365 (p) REVERT: C 388 ASN cc_start: 0.8770 (p0) cc_final: 0.8375 (m-40) REVERT: C 402 ILE cc_start: 0.8619 (pt) cc_final: 0.8337 (pt) REVERT: C 414 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8177 (tm-30) REVERT: C 697 MET cc_start: 0.8305 (ptm) cc_final: 0.7729 (ttp) REVERT: C 731 MET cc_start: 0.8911 (ptm) cc_final: 0.8528 (ptp) REVERT: C 869 MET cc_start: 0.8933 (mtt) cc_final: 0.8552 (mtp) REVERT: C 936 ASP cc_start: 0.8772 (t70) cc_final: 0.8551 (t0) REVERT: D 83 MET cc_start: -0.6558 (mmt) cc_final: -0.8104 (mtt) REVERT: D 110 MET cc_start: 0.5382 (mmp) cc_final: 0.4391 (mmp) REVERT: F 83 MET cc_start: -0.6255 (mmt) cc_final: -0.7861 (mtt) REVERT: F 110 MET cc_start: 0.5215 (mmp) cc_final: 0.4418 (mmp) REVERT: H 110 MET cc_start: 0.5776 (mmp) cc_final: 0.4919 (mmp) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1675 time to fit residues: 53.8651 Evaluate side-chains 138 residues out of total 3336 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 304 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 350 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 174 optimal weight: 0.7980 chunk 348 optimal weight: 50.0000 chunk 345 optimal weight: 0.0370 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 519 HIS A1005 GLN C 519 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.132258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081717 restraints weight = 108789.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.081489 restraints weight = 73438.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.081742 restraints weight = 44637.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.082108 restraints weight = 40946.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.082255 restraints weight = 37283.174| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31434 Z= 0.125 Angle : 0.517 11.416 42864 Z= 0.268 Chirality : 0.042 0.212 4935 Planarity : 0.003 0.043 5451 Dihedral : 3.874 18.115 4155 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.14), residues: 3798 helix: 1.34 (0.20), residues: 705 sheet: 0.65 (0.16), residues: 990 loop : -0.25 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.033 0.001 TYR A 369 PHE 0.021 0.001 PHE C 906 TRP 0.007 0.001 TRP D 36 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (31332) covalent geometry : angle 0.50979 / 0.27 (42606) SS BOND : bond 0.00411 / 0.28 ( 48) SS BOND : angle 1.35637 / 0.96 ( 96) hydrogen bonds : bond 0.03767 / 2.50 ( 1229) hydrogen bonds : angle 5.12640 / 3.56 ( 3381) link_BETA1-4 : bond 0.00272 / 0.15 ( 15) link_BETA1-4 : angle 0.97725 / 0.67 ( 45) link_NAG-ASN : bond 0.00176 / 0.11 ( 39) link_NAG-ASN : angle 1.14915 / 0.76 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4996.67 seconds wall clock time: 87 minutes 28.47 seconds (5248.47 seconds total)