Starting phenix.real_space_refine on Tue Aug 26 01:22:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aru_43794/08_2025/9aru_43794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aru_43794/08_2025/9aru_43794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9aru_43794/08_2025/9aru_43794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aru_43794/08_2025/9aru_43794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9aru_43794/08_2025/9aru_43794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aru_43794/08_2025/9aru_43794.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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 156 5.16 5 C 20211 2.51 5 N 5280 2.21 5 O 6279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31926 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8519 Classifications: {'peptide': 1092} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 864 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "B" Number of atoms: 8519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8519 Classifications: {'peptide': 1092} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "F" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 864 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "C" Number of atoms: 8519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8519 Classifications: {'peptide': 1092} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 56, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "G" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 864 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.38, per 1000 atoms: 0.23 Number of scatterers: 31926 At special positions: 0 Unit cell: (146.05, 135.7, 208.15, 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 156 16.00 O 6279 8.00 N 5280 7.00 C 20211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.01 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " 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 H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100C" distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " 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 D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 100C" distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " 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 E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 100C" distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 17 " " NAG A1309 " - " ASN A 61 " " NAG B1301 " - " ASN B 122 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 17 " " NAG B1309 " - " ASN B 61 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 17 " " NAG C1309 " - " ASN C 61 " " 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 A1074 " " NAG P 1 " - " ASN B 234 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN C 234 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " " NAG a 1 " - " ASN C1074 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.7 microseconds 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7386 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 72 sheets defined 22.5% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.688A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 4.025A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.885A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.356A 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: 3.617A 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 756 through 783 removed outlier: 3.667A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.645A 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 848 through 856 removed outlier: 3.698A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.618A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.166A 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 945 through 967 removed outlier: 4.025A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 76 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.516A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.687A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 4.025A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.880A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.354A 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: 3.626A 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 756 through 783 removed outlier: 3.667A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.646A 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 848 through 856 removed outlier: 3.696A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.618A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.171A 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 945 through 967 removed outlier: 4.025A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.520A pdb=" N VAL F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.685A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 4.024A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.882A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.357A 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: 3.603A 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 756 through 783 removed outlier: 3.670A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.646A 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 848 through 856 removed outlier: 3.701A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.614A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.168A 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 945 through 967 removed outlier: 4.018A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.520A pdb=" N VAL G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.744A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.259A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.702A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.139A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.845A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.255A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.269A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.269A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.877A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 5.318A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.996A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.560A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.460A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 796 through 797 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.422A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.577A pdb=" N ALA H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP H 36 " --> pdb=" O ALA H 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.101A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.512A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.544A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.160A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.735A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AD2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.707A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.132A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.840A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AD6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.251A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.272A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.272A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.870A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AE4, first strand: chain 'B' and resid 711 through 715 removed outlier: 5.319A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.976A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.566A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 796 through 797 Processing sheet with id=AE8, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.419A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.597A pdb=" N ALA D 33 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP D 36 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 12 removed outlier: 7.100A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.528A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.507A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.144A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.740A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.704A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.136A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.827A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AG3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.273A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.273A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 711 through 715 removed outlier: 5.322A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.987A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.567A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 796 through 797 Processing sheet with id=AH3, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.420A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AH5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.596A pdb=" N ALA E 33 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET E 34 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TRP E 36 " --> pdb=" O ALA E 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 10 through 12 removed outlier: 7.139A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.522A pdb=" N SER G 67 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.506A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.123A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) 1389 hydrogen bonds defined for protein. 3681 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: 9.69 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10106 1.34 - 1.47: 8305 1.47 - 1.59: 14028 1.59 - 1.71: 0 1.71 - 1.83: 198 Bond restraints: 32637 Sorted by residual: bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N ASP G 1 " pdb=" CA ASP G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N GLN D 1 " pdb=" CA GLN D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.76e+00 ... (remaining 32632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 41266 1.91 - 3.82: 2663 3.82 - 5.72: 407 5.72 - 7.63: 37 7.63 - 9.54: 6 Bond angle restraints: 44379 Sorted by residual: angle pdb=" CA CYS B 760 " pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 114.40 123.94 -9.54 2.30e+00 1.89e-01 1.72e+01 angle pdb=" N PHE C 515 " pdb=" CA PHE C 515 " pdb=" C PHE C 515 " ideal model delta sigma weight residual 108.79 115.12 -6.33 1.53e+00 4.27e-01 1.71e+01 angle pdb=" N PHE A 515 " pdb=" CA PHE A 515 " pdb=" C PHE A 515 " ideal model delta sigma weight residual 108.79 115.10 -6.31 1.53e+00 4.27e-01 1.70e+01 angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 123.88 -9.48 2.30e+00 1.89e-01 1.70e+01 angle pdb=" N PHE B 515 " pdb=" CA PHE B 515 " pdb=" C PHE B 515 " ideal model delta sigma weight residual 108.79 115.09 -6.30 1.53e+00 4.27e-01 1.70e+01 ... (remaining 44374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 19477 17.94 - 35.88: 550 35.88 - 53.83: 175 53.83 - 71.77: 24 71.77 - 89.71: 21 Dihedral angle restraints: 20247 sinusoidal: 8712 harmonic: 11535 Sorted by residual: dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 52.55 40.45 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 52.60 40.40 1 1.00e+01 1.00e-02 2.29e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 52.62 40.38 1 1.00e+01 1.00e-02 2.29e+01 ... (remaining 20244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3793 0.060 - 0.120: 1046 0.120 - 0.180: 277 0.180 - 0.240: 32 0.240 - 0.300: 3 Chirality restraints: 5151 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.29e+00 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.94e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 5148 not shown) Planarity restraints: 5727 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 7 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C SER D 7 " 0.064 2.00e-02 2.50e+03 pdb=" O SER D 7 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY D 8 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 7 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.34e+01 pdb=" C SER E 7 " 0.063 2.00e-02 2.50e+03 pdb=" O SER E 7 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY E 8 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 7 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C SER H 7 " -0.063 2.00e-02 2.50e+03 pdb=" O SER H 7 " 0.024 2.00e-02 2.50e+03 pdb=" N GLY H 8 " 0.021 2.00e-02 2.50e+03 ... (remaining 5724 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1874 2.73 - 3.27: 30656 3.27 - 3.81: 51557 3.81 - 4.36: 64088 4.36 - 4.90: 108696 Nonbonded interactions: 256871 Sorted by model distance: nonbonded pdb=" ND2 ASN B 317 " pdb=" OD2 ASP C 737 " model vdw 2.181 3.120 nonbonded pdb=" ND2 ASN A 317 " pdb=" OD2 ASP B 737 " model vdw 2.181 3.120 nonbonded pdb=" OD2 ASP A 737 " pdb=" ND2 ASN C 317 " model vdw 2.185 3.120 nonbonded pdb=" O ARG B 214 " pdb=" OH TYR B 266 " model vdw 2.244 3.040 nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.247 3.040 ... (remaining 256866 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' 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' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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: 6.480 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: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 33.190 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.180 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.006 0.050 32754 Z= 0.256 Angle : 1.060 12.262 44676 Z= 0.613 Chirality : 0.059 0.300 5151 Planarity : 0.005 0.043 5682 Dihedral : 9.891 89.709 12699 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 0.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.09 % Allowed : 0.52 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.12), residues: 3948 helix: 1.22 (0.18), residues: 669 sheet: 1.01 (0.17), residues: 876 loop : 0.27 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 567 TYR 0.027 0.003 TYR B 756 PHE 0.021 0.003 PHE A 133 TRP 0.019 0.003 TRP D 36 HIS 0.010 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00568 (32637) covalent geometry : angle 1.04468 (44379) SS BOND : bond 0.00737 ( 54) SS BOND : angle 2.35853 ( 108) hydrogen bonds : bond 0.14639 ( 1317) hydrogen bonds : angle 7.52950 ( 3681) link_BETA1-4 : bond 0.01272 ( 18) link_BETA1-4 : angle 3.49538 ( 54) link_NAG-ASN : bond 0.00406 ( 45) link_NAG-ASN : angle 1.92717 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 840 time to evaluate : 1.196 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 58 PHE cc_start: 0.7659 (m-10) cc_final: 0.7366 (m-80) REVERT: A 140 PHE cc_start: 0.7967 (p90) cc_final: 0.7695 (p90) REVERT: A 223 LEU cc_start: 0.8019 (mt) cc_final: 0.7759 (mp) REVERT: A 269 TYR cc_start: 0.6756 (m-80) cc_final: 0.6498 (m-80) REVERT: A 276 LEU cc_start: 0.8920 (tp) cc_final: 0.8673 (tt) REVERT: A 289 VAL cc_start: 0.8641 (t) cc_final: 0.8228 (p) REVERT: A 353 TRP cc_start: 0.8597 (p-90) cc_final: 0.7733 (p-90) REVERT: A 400 PHE cc_start: 0.7540 (p90) cc_final: 0.7305 (p90) REVERT: A 402 ILE cc_start: 0.7641 (pt) cc_final: 0.6991 (pt) REVERT: A 495 TYR cc_start: 0.6187 (m-80) cc_final: 0.5815 (m-80) REVERT: A 562 PHE cc_start: 0.7111 (p90) cc_final: 0.6853 (p90) REVERT: A 762 GLN cc_start: 0.8991 (tt0) cc_final: 0.8613 (tm-30) REVERT: A 869 MET cc_start: 0.8963 (mtt) cc_final: 0.8731 (mtt) REVERT: A 909 ILE cc_start: 0.8225 (mm) cc_final: 0.8012 (mm) REVERT: A 945 LEU cc_start: 0.8412 (mt) cc_final: 0.8156 (mt) REVERT: A 1011 GLN cc_start: 0.8707 (tp40) cc_final: 0.8101 (tp40) REVERT: A 1071 GLN cc_start: 0.8485 (mp10) cc_final: 0.8242 (mp10) REVERT: H 34 MET cc_start: 0.6372 (mtp) cc_final: 0.6012 (mtp) REVERT: H 59 TYR cc_start: 0.8151 (m-80) cc_final: 0.7323 (m-10) REVERT: H 72 ASP cc_start: 0.7370 (t0) cc_final: 0.6476 (p0) REVERT: H 77 THR cc_start: 0.8440 (m) cc_final: 0.8050 (m) REVERT: L 4 MET cc_start: 0.7760 (tpp) cc_final: 0.7296 (tpt) REVERT: L 21 ILE cc_start: 0.8419 (mt) cc_final: 0.8197 (tt) REVERT: L 35 TRP cc_start: 0.6609 (m100) cc_final: 0.6146 (m100) REVERT: L 104 LEU cc_start: 0.9139 (tt) cc_final: 0.8930 (tt) REVERT: B 140 PHE cc_start: 0.7936 (p90) cc_final: 0.7666 (p90) REVERT: B 177 MET cc_start: 0.5734 (mmt) cc_final: 0.5482 (mmm) REVERT: B 223 LEU cc_start: 0.8161 (mt) cc_final: 0.7736 (tp) REVERT: B 267 VAL cc_start: 0.7869 (t) cc_final: 0.6937 (t) REVERT: B 289 VAL cc_start: 0.8609 (t) cc_final: 0.8206 (p) REVERT: B 353 TRP cc_start: 0.8670 (p-90) cc_final: 0.7603 (p-90) REVERT: B 392 PHE cc_start: 0.7658 (m-80) cc_final: 0.7139 (m-80) REVERT: B 402 ILE cc_start: 0.7755 (pt) cc_final: 0.7390 (pt) REVERT: B 495 TYR cc_start: 0.6443 (m-80) cc_final: 0.6098 (m-80) REVERT: B 562 PHE cc_start: 0.7563 (p90) cc_final: 0.7137 (p90) REVERT: B 785 VAL cc_start: 0.9505 (t) cc_final: 0.8918 (p) REVERT: B 824 ASN cc_start: 0.8707 (m-40) cc_final: 0.8457 (t0) REVERT: B 945 LEU cc_start: 0.8635 (mt) cc_final: 0.8378 (mt) REVERT: B 990 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7631 (tm-30) REVERT: B 1011 GLN cc_start: 0.8678 (tp40) cc_final: 0.8057 (tp40) REVERT: D 59 TYR cc_start: 0.8139 (m-80) cc_final: 0.7635 (m-10) REVERT: D 72 ASP cc_start: 0.7200 (t0) cc_final: 0.6065 (p0) REVERT: D 77 THR cc_start: 0.8301 (m) cc_final: 0.7197 (p) REVERT: D 79 TYR cc_start: 0.7490 (m-80) cc_final: 0.7053 (m-80) REVERT: F 4 MET cc_start: 0.7520 (tpp) cc_final: 0.6848 (tpt) REVERT: F 35 TRP cc_start: 0.6683 (m100) cc_final: 0.6325 (m100) REVERT: F 93 HIS cc_start: 0.8501 (m90) cc_final: 0.8006 (m90) REVERT: C 140 PHE cc_start: 0.7945 (p90) cc_final: 0.6859 (p90) REVERT: C 177 MET cc_start: 0.5403 (mmt) cc_final: 0.5191 (mmm) REVERT: C 223 LEU cc_start: 0.8170 (mt) cc_final: 0.7952 (mp) REVERT: C 240 THR cc_start: 0.8815 (p) cc_final: 0.8593 (p) REVERT: C 276 LEU cc_start: 0.8921 (tp) cc_final: 0.8540 (tt) REVERT: C 289 VAL cc_start: 0.8672 (t) cc_final: 0.8181 (p) REVERT: C 353 TRP cc_start: 0.8713 (p-90) cc_final: 0.7823 (p-90) REVERT: C 400 PHE cc_start: 0.7167 (p90) cc_final: 0.6953 (p90) REVERT: C 402 ILE cc_start: 0.7605 (pt) cc_final: 0.7036 (pt) REVERT: C 434 ILE cc_start: 0.8166 (mt) cc_final: 0.7938 (mp) REVERT: C 495 TYR cc_start: 0.6655 (m-80) cc_final: 0.5979 (m-80) REVERT: C 562 PHE cc_start: 0.7327 (p90) cc_final: 0.7085 (p90) REVERT: C 664 ILE cc_start: 0.7887 (mt) cc_final: 0.7649 (tt) REVERT: C 856 ASN cc_start: 0.9131 (m-40) cc_final: 0.8832 (m110) REVERT: C 869 MET cc_start: 0.8992 (mtt) cc_final: 0.8790 (mtt) REVERT: C 945 LEU cc_start: 0.8539 (mt) cc_final: 0.8285 (mt) REVERT: C 1011 GLN cc_start: 0.8749 (tp40) cc_final: 0.8190 (tp40) REVERT: E 3 GLN cc_start: 0.8831 (tp40) cc_final: 0.8461 (tp-100) REVERT: E 29 PHE cc_start: 0.7209 (t80) cc_final: 0.6892 (t80) REVERT: E 72 ASP cc_start: 0.7055 (t0) cc_final: 0.6820 (t0) REVERT: G 4 MET cc_start: 0.7883 (tpp) cc_final: 0.7198 (tpt) REVERT: G 93 HIS cc_start: 0.8541 (m90) cc_final: 0.8255 (m90) outliers start: 3 outliers final: 0 residues processed: 843 average time/residue: 0.2272 time to fit residues: 294.2279 Evaluate side-chains 406 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN A 501 ASN A 580 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 501 ASN B 580 GLN B 762 GLN F 53 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 501 ASN C 580 GLN E 1 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.104268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.079010 restraints weight = 95449.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.081919 restraints weight = 47635.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.083865 restraints weight = 29953.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.085152 restraints weight = 21794.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.085948 restraints weight = 17561.631| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32754 Z= 0.152 Angle : 0.713 13.370 44676 Z= 0.368 Chirality : 0.046 0.244 5151 Planarity : 0.005 0.092 5682 Dihedral : 5.463 54.955 5628 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.91 % Allowed : 8.45 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.13), residues: 3948 helix: 2.41 (0.19), residues: 675 sheet: 0.83 (0.15), residues: 939 loop : -0.09 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 39 TYR 0.026 0.002 TYR B 265 PHE 0.030 0.002 PHE D 67 TRP 0.015 0.001 TRP B 104 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00331 (32637) covalent geometry : angle 0.69029 (44379) SS BOND : bond 0.00381 ( 54) SS BOND : angle 1.74558 ( 108) hydrogen bonds : bond 0.05246 ( 1317) hydrogen bonds : angle 6.21041 ( 3681) link_BETA1-4 : bond 0.00556 ( 18) link_BETA1-4 : angle 1.91729 ( 54) link_NAG-ASN : bond 0.00599 ( 45) link_NAG-ASN : angle 2.74552 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 487 time to evaluate : 1.234 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: symmetry clash REVERT: A 135 PHE cc_start: 0.7827 (m-80) cc_final: 0.7618 (m-80) REVERT: A 140 PHE cc_start: 0.7841 (p90) cc_final: 0.7192 (p90) REVERT: A 177 MET cc_start: 0.6409 (mmm) cc_final: 0.6090 (mmm) REVERT: A 200 TYR cc_start: 0.8449 (m-80) cc_final: 0.7998 (m-80) REVERT: A 223 LEU cc_start: 0.7971 (mt) cc_final: 0.7695 (mp) REVERT: A 237 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7643 (mtm110) REVERT: A 269 TYR cc_start: 0.6909 (m-80) cc_final: 0.6627 (m-80) REVERT: A 276 LEU cc_start: 0.8986 (tp) cc_final: 0.8775 (tt) REVERT: A 289 VAL cc_start: 0.8809 (t) cc_final: 0.8508 (p) REVERT: A 402 ILE cc_start: 0.7658 (pt) cc_final: 0.7290 (pt) REVERT: A 473 TYR cc_start: 0.8297 (m-10) cc_final: 0.7982 (m-10) REVERT: A 495 TYR cc_start: 0.6229 (m-80) cc_final: 0.5834 (m-80) REVERT: A 759 PHE cc_start: 0.8428 (m-10) cc_final: 0.7988 (m-80) REVERT: A 869 MET cc_start: 0.9043 (mtt) cc_final: 0.8839 (mtt) REVERT: A 968 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8512 (t) REVERT: A 993 ILE cc_start: 0.8914 (mt) cc_final: 0.8701 (tt) REVERT: A 1011 GLN cc_start: 0.8767 (tp40) cc_final: 0.8280 (tp40) REVERT: H 59 TYR cc_start: 0.8072 (m-80) cc_final: 0.7337 (m-10) REVERT: H 72 ASP cc_start: 0.7594 (t0) cc_final: 0.6409 (p0) REVERT: L 4 MET cc_start: 0.8024 (tpp) cc_final: 0.7575 (tpt) REVERT: L 35 TRP cc_start: 0.6404 (m100) cc_final: 0.6141 (m100) REVERT: L 54 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8272 (tpt-90) REVERT: L 83 VAL cc_start: 0.9093 (m) cc_final: 0.8836 (t) REVERT: B 104 TRP cc_start: 0.8400 (m-90) cc_final: 0.6809 (m100) REVERT: B 140 PHE cc_start: 0.7879 (p90) cc_final: 0.7608 (p90) REVERT: B 200 TYR cc_start: 0.8581 (m-80) cc_final: 0.8234 (m-80) REVERT: B 223 LEU cc_start: 0.8145 (mt) cc_final: 0.7909 (mp) REVERT: B 289 VAL cc_start: 0.8831 (t) cc_final: 0.8621 (p) REVERT: B 392 PHE cc_start: 0.7721 (m-80) cc_final: 0.7328 (m-80) REVERT: B 402 ILE cc_start: 0.7889 (pt) cc_final: 0.7563 (pt) REVERT: B 495 TYR cc_start: 0.6355 (m-80) cc_final: 0.5882 (m-80) REVERT: B 990 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7706 (tm-30) REVERT: B 1011 GLN cc_start: 0.8833 (tp40) cc_final: 0.8320 (tp40) REVERT: D 59 TYR cc_start: 0.8023 (m-80) cc_final: 0.7434 (m-80) REVERT: D 72 ASP cc_start: 0.7313 (t0) cc_final: 0.6296 (p0) REVERT: F 86 TYR cc_start: 0.8739 (m-10) cc_final: 0.8509 (m-10) REVERT: F 93 HIS cc_start: 0.8562 (m90) cc_final: 0.8038 (m-70) REVERT: C 140 PHE cc_start: 0.7805 (p90) cc_final: 0.7073 (p90) REVERT: C 223 LEU cc_start: 0.8104 (mt) cc_final: 0.7870 (mp) REVERT: C 269 TYR cc_start: 0.7165 (m-80) cc_final: 0.6175 (m-80) REVERT: C 276 LEU cc_start: 0.9017 (tp) cc_final: 0.8684 (tt) REVERT: C 289 VAL cc_start: 0.8946 (t) cc_final: 0.8580 (p) REVERT: C 402 ILE cc_start: 0.7750 (pt) cc_final: 0.7526 (pt) REVERT: C 473 TYR cc_start: 0.8109 (m-10) cc_final: 0.7807 (m-10) REVERT: C 495 TYR cc_start: 0.6606 (m-80) cc_final: 0.5918 (m-80) REVERT: C 707 TYR cc_start: 0.6699 (t80) cc_final: 0.6467 (t80) REVERT: C 869 MET cc_start: 0.9127 (mtt) cc_final: 0.8706 (mtt) REVERT: C 1011 GLN cc_start: 0.8730 (tp40) cc_final: 0.8443 (tp40) REVERT: E 1 GLN cc_start: 0.8439 (tm130) cc_final: 0.7885 (tm-30) REVERT: E 3 GLN cc_start: 0.8986 (tp40) cc_final: 0.8714 (tp40) REVERT: E 72 ASP cc_start: 0.6965 (t0) cc_final: 0.6662 (t0) REVERT: E 75 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8968 (mmmt) REVERT: E 83 ARG cc_start: 0.8132 (mpt180) cc_final: 0.7767 (mpt180) REVERT: G 4 MET cc_start: 0.7847 (tpp) cc_final: 0.7359 (tpt) REVERT: G 54 ARG cc_start: 0.8725 (ttt90) cc_final: 0.8164 (tpp-160) REVERT: G 93 HIS cc_start: 0.8624 (m90) cc_final: 0.8179 (m-70) outliers start: 66 outliers final: 33 residues processed: 530 average time/residue: 0.2013 time to fit residues: 171.0685 Evaluate side-chains 410 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 375 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 54 ARG Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 705 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1006 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 109 optimal weight: 9.9990 chunk 290 optimal weight: 3.9990 chunk 344 optimal weight: 0.0270 chunk 268 optimal weight: 4.9990 chunk 343 optimal weight: 10.0000 chunk 312 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 202 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS A1142 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B1048 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1010 GLN C1048 HIS C1054 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.074045 restraints weight = 99534.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076721 restraints weight = 51751.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.078485 restraints weight = 33714.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.079589 restraints weight = 25300.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.080416 restraints weight = 20908.504| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 32754 Z= 0.243 Angle : 0.737 11.907 44676 Z= 0.376 Chirality : 0.046 0.242 5151 Planarity : 0.005 0.065 5682 Dihedral : 5.530 52.714 5628 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.50 % Favored : 96.43 % Rotamer: Outliers : 3.07 % Allowed : 9.03 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.13), residues: 3948 helix: 2.26 (0.20), residues: 672 sheet: 0.68 (0.16), residues: 939 loop : -0.40 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1107 TYR 0.045 0.002 TYR F 49 PHE 0.044 0.002 PHE H 67 TRP 0.011 0.002 TRP C 436 HIS 0.008 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00555 (32637) covalent geometry : angle 0.71713 (44379) SS BOND : bond 0.00505 ( 54) SS BOND : angle 1.86571 ( 108) hydrogen bonds : bond 0.05109 ( 1317) hydrogen bonds : angle 6.01530 ( 3681) link_BETA1-4 : bond 0.00401 ( 18) link_BETA1-4 : angle 1.73249 ( 54) link_NAG-ASN : bond 0.00504 ( 45) link_NAG-ASN : angle 2.55657 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 371 time to evaluate : 1.313 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: A 138 ASP cc_start: 0.7800 (m-30) cc_final: 0.7078 (p0) REVERT: A 140 PHE cc_start: 0.7836 (p90) cc_final: 0.7603 (p90) REVERT: A 177 MET cc_start: 0.5853 (mmm) cc_final: 0.5450 (mmm) REVERT: A 200 TYR cc_start: 0.8555 (m-80) cc_final: 0.8215 (m-80) REVERT: A 223 LEU cc_start: 0.8173 (mt) cc_final: 0.7847 (mp) REVERT: A 269 TYR cc_start: 0.7102 (m-80) cc_final: 0.6831 (m-80) REVERT: A 289 VAL cc_start: 0.8889 (t) cc_final: 0.8638 (p) REVERT: A 318 PHE cc_start: 0.7085 (t80) cc_final: 0.6581 (t80) REVERT: A 402 ILE cc_start: 0.7851 (pt) cc_final: 0.7540 (pt) REVERT: A 436 TRP cc_start: 0.7833 (p90) cc_final: 0.7606 (p-90) REVERT: A 473 TYR cc_start: 0.8347 (m-10) cc_final: 0.7892 (m-10) REVERT: A 495 TYR cc_start: 0.6517 (m-80) cc_final: 0.6060 (m-80) REVERT: A 664 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7847 (tt) REVERT: A 755 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8385 (mp10) REVERT: A 762 GLN cc_start: 0.9132 (tt0) cc_final: 0.8655 (tm-30) REVERT: A 984 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 1011 GLN cc_start: 0.8952 (tp40) cc_final: 0.8470 (tp40) REVERT: H 72 ASP cc_start: 0.7529 (t0) cc_final: 0.6405 (p0) REVERT: H 100 ASP cc_start: 0.8648 (t0) cc_final: 0.8356 (t0) REVERT: L 4 MET cc_start: 0.8029 (tpp) cc_final: 0.7611 (tpt) REVERT: L 35 TRP cc_start: 0.6535 (m100) cc_final: 0.6307 (m100) REVERT: L 89 MET cc_start: 0.5430 (ttp) cc_final: 0.5070 (tmm) REVERT: B 138 ASP cc_start: 0.7831 (m-30) cc_final: 0.7487 (p0) REVERT: B 200 TYR cc_start: 0.8593 (m-80) cc_final: 0.8274 (m-80) REVERT: B 223 LEU cc_start: 0.8128 (mt) cc_final: 0.7761 (tp) REVERT: B 289 VAL cc_start: 0.8892 (t) cc_final: 0.8645 (p) REVERT: B 402 ILE cc_start: 0.7981 (pt) cc_final: 0.7675 (pt) REVERT: B 495 TYR cc_start: 0.6583 (m-80) cc_final: 0.5884 (m-80) REVERT: B 664 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7724 (tt) REVERT: B 869 MET cc_start: 0.9013 (mtt) cc_final: 0.8756 (mtt) REVERT: B 990 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7714 (tm-30) REVERT: B 1011 GLN cc_start: 0.9005 (tp40) cc_final: 0.8537 (tp40) REVERT: D 72 ASP cc_start: 0.7446 (t0) cc_final: 0.6185 (p0) REVERT: D 82 MET cc_start: 0.6723 (mtm) cc_final: 0.6522 (mtm) REVERT: F 83 VAL cc_start: 0.9128 (m) cc_final: 0.8858 (t) REVERT: F 93 HIS cc_start: 0.8646 (m90) cc_final: 0.8149 (m-70) REVERT: C 138 ASP cc_start: 0.7698 (m-30) cc_final: 0.7072 (p0) REVERT: C 140 PHE cc_start: 0.7932 (p90) cc_final: 0.6622 (p90) REVERT: C 177 MET cc_start: 0.5894 (mmt) cc_final: 0.5620 (mmt) REVERT: C 200 TYR cc_start: 0.8498 (m-80) cc_final: 0.8268 (m-80) REVERT: C 223 LEU cc_start: 0.8090 (mt) cc_final: 0.7812 (mp) REVERT: C 289 VAL cc_start: 0.8932 (t) cc_final: 0.8640 (p) REVERT: C 473 TYR cc_start: 0.8106 (m-10) cc_final: 0.7691 (m-10) REVERT: C 869 MET cc_start: 0.9137 (mtt) cc_final: 0.8768 (mtt) REVERT: C 984 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8245 (mp) REVERT: E 3 GLN cc_start: 0.9061 (tp40) cc_final: 0.8604 (tp-100) REVERT: E 72 ASP cc_start: 0.7049 (t0) cc_final: 0.6636 (t0) REVERT: G 4 MET cc_start: 0.8071 (tpp) cc_final: 0.7737 (tpt) REVERT: G 35 TRP cc_start: 0.6883 (m100) cc_final: 0.6619 (m100) REVERT: G 42 GLN cc_start: 0.9204 (mt0) cc_final: 0.8874 (mp10) REVERT: G 50 GLN cc_start: 0.9151 (mp10) cc_final: 0.8933 (pm20) REVERT: G 53 ASN cc_start: 0.8926 (t0) cc_final: 0.8676 (t0) REVERT: G 54 ARG cc_start: 0.8793 (ttt90) cc_final: 0.8276 (tpp-160) REVERT: G 75 ILE cc_start: 0.6585 (OUTLIER) cc_final: 0.6217 (mt) REVERT: G 93 HIS cc_start: 0.8841 (m90) cc_final: 0.8465 (m-70) outliers start: 106 outliers final: 62 residues processed: 449 average time/residue: 0.2156 time to fit residues: 155.9709 Evaluate side-chains 386 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 318 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 257 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 189 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 233 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.102108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.075139 restraints weight = 98556.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.077862 restraints weight = 50898.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079679 restraints weight = 32944.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.080856 restraints weight = 24566.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.081588 restraints weight = 20190.171| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32754 Z= 0.151 Angle : 0.642 10.230 44676 Z= 0.325 Chirality : 0.045 0.224 5151 Planarity : 0.004 0.072 5682 Dihedral : 5.420 54.617 5628 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 2.72 % Allowed : 10.59 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.13), residues: 3948 helix: 2.57 (0.20), residues: 654 sheet: 0.61 (0.16), residues: 939 loop : -0.53 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 83 TYR 0.033 0.001 TYR L 49 PHE 0.054 0.002 PHE H 67 TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00342 (32637) covalent geometry : angle 0.62889 (44379) SS BOND : bond 0.00306 ( 54) SS BOND : angle 1.45575 ( 108) hydrogen bonds : bond 0.04528 ( 1317) hydrogen bonds : angle 5.65687 ( 3681) link_BETA1-4 : bond 0.00445 ( 18) link_BETA1-4 : angle 1.48673 ( 54) link_NAG-ASN : bond 0.00265 ( 45) link_NAG-ASN : angle 1.95381 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 362 time to evaluate : 1.242 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: A 140 PHE cc_start: 0.7916 (p90) cc_final: 0.7522 (p90) REVERT: A 177 MET cc_start: 0.5829 (mmm) cc_final: 0.4983 (mmm) REVERT: A 200 TYR cc_start: 0.8458 (m-80) cc_final: 0.8247 (m-80) REVERT: A 223 LEU cc_start: 0.8168 (mt) cc_final: 0.7578 (tp) REVERT: A 269 TYR cc_start: 0.7062 (m-80) cc_final: 0.6801 (m-80) REVERT: A 289 VAL cc_start: 0.8939 (t) cc_final: 0.8576 (p) REVERT: A 318 PHE cc_start: 0.6985 (t80) cc_final: 0.6348 (t80) REVERT: A 402 ILE cc_start: 0.7787 (pt) cc_final: 0.7411 (pt) REVERT: A 473 TYR cc_start: 0.8283 (m-10) cc_final: 0.7755 (m-10) REVERT: A 495 TYR cc_start: 0.6658 (m-80) cc_final: 0.5810 (m-80) REVERT: A 664 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7931 (tt) REVERT: A 762 GLN cc_start: 0.9082 (tt0) cc_final: 0.8625 (tm-30) REVERT: A 869 MET cc_start: 0.8910 (mtt) cc_final: 0.8480 (mtt) REVERT: A 934 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8612 (tt) REVERT: A 984 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8148 (mp) REVERT: H 72 ASP cc_start: 0.7613 (t0) cc_final: 0.6552 (p0) REVERT: H 100 ASP cc_start: 0.8620 (t0) cc_final: 0.8313 (t0) REVERT: L 4 MET cc_start: 0.7978 (tpp) cc_final: 0.7552 (tpt) REVERT: L 35 TRP cc_start: 0.6494 (m100) cc_final: 0.6153 (m100) REVERT: L 42 GLN cc_start: 0.9085 (mt0) cc_final: 0.8732 (mp10) REVERT: L 74 LYS cc_start: 0.8752 (mmtt) cc_final: 0.8503 (mttt) REVERT: L 75 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6656 (mt) REVERT: L 89 MET cc_start: 0.5356 (ttp) cc_final: 0.4951 (tmm) REVERT: B 138 ASP cc_start: 0.7814 (m-30) cc_final: 0.7395 (p0) REVERT: B 177 MET cc_start: 0.6136 (mmt) cc_final: 0.5799 (mmt) REVERT: B 223 LEU cc_start: 0.8481 (mt) cc_final: 0.7916 (tp) REVERT: B 289 VAL cc_start: 0.8808 (t) cc_final: 0.8561 (p) REVERT: B 402 ILE cc_start: 0.7852 (pt) cc_final: 0.7604 (pt) REVERT: B 473 TYR cc_start: 0.7870 (m-10) cc_final: 0.7450 (m-10) REVERT: B 664 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 869 MET cc_start: 0.8988 (mtt) cc_final: 0.8712 (mtt) REVERT: B 990 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7662 (tm-30) REVERT: D 38 ARG cc_start: 0.8709 (ptt180) cc_final: 0.8248 (ptt-90) REVERT: D 72 ASP cc_start: 0.7423 (t0) cc_final: 0.6252 (p0) REVERT: D 83 ARG cc_start: 0.6728 (mpt-90) cc_final: 0.6403 (mtm-85) REVERT: D 85 GLU cc_start: 0.7521 (pm20) cc_final: 0.6936 (mp0) REVERT: F 54 ARG cc_start: 0.8666 (ttt90) cc_final: 0.7862 (tpt-90) REVERT: F 74 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8545 (tttt) REVERT: F 75 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6499 (mt) REVERT: F 93 HIS cc_start: 0.8668 (m90) cc_final: 0.8214 (m-70) REVERT: C 138 ASP cc_start: 0.7690 (m-30) cc_final: 0.6944 (p0) REVERT: C 140 PHE cc_start: 0.8018 (p90) cc_final: 0.7118 (p90) REVERT: C 177 MET cc_start: 0.5779 (mmt) cc_final: 0.5477 (mmt) REVERT: C 223 LEU cc_start: 0.8196 (mt) cc_final: 0.7949 (mp) REVERT: C 289 VAL cc_start: 0.8913 (t) cc_final: 0.8613 (p) REVERT: C 473 TYR cc_start: 0.8188 (m-10) cc_final: 0.7694 (m-10) REVERT: C 495 TYR cc_start: 0.7078 (m-80) cc_final: 0.5974 (m-80) REVERT: C 497 PHE cc_start: 0.7540 (m-10) cc_final: 0.7268 (m-80) REVERT: C 869 MET cc_start: 0.9165 (mtt) cc_final: 0.8782 (mtt) REVERT: E 3 GLN cc_start: 0.9128 (tp40) cc_final: 0.8660 (tp-100) REVERT: E 72 ASP cc_start: 0.7139 (t0) cc_final: 0.6621 (t0) REVERT: E 75 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8751 (mmmt) REVERT: E 100 ASP cc_start: 0.8444 (t0) cc_final: 0.8100 (t0) REVERT: G 4 MET cc_start: 0.8146 (tpp) cc_final: 0.7748 (tpt) REVERT: G 50 GLN cc_start: 0.9288 (mp10) cc_final: 0.9017 (mp10) REVERT: G 53 ASN cc_start: 0.8847 (t0) cc_final: 0.8394 (t0) REVERT: G 89 MET cc_start: 0.5497 (ttp) cc_final: 0.5242 (tmm) REVERT: G 93 HIS cc_start: 0.8818 (m90) cc_final: 0.8440 (m-70) outliers start: 94 outliers final: 61 residues processed: 428 average time/residue: 0.2202 time to fit residues: 151.8312 Evaluate side-chains 373 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 306 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 705 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 3 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 115 optimal weight: 0.0770 chunk 149 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 300 optimal weight: 0.8980 chunk 204 optimal weight: 3.9990 chunk 362 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A1054 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 762 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 901 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.100375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074661 restraints weight = 95191.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.077336 restraints weight = 49141.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.079135 restraints weight = 31676.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.080231 restraints weight = 23504.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081084 restraints weight = 19347.060| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32754 Z= 0.124 Angle : 0.618 9.624 44676 Z= 0.311 Chirality : 0.044 0.239 5151 Planarity : 0.004 0.040 5682 Dihedral : 5.299 54.981 5628 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 2.40 % Allowed : 11.95 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.13), residues: 3948 helix: 2.72 (0.20), residues: 654 sheet: 0.65 (0.16), residues: 933 loop : -0.58 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 38 TYR 0.031 0.001 TYR A 904 PHE 0.048 0.002 PHE B 497 TRP 0.010 0.001 TRP G 35 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00279 (32637) covalent geometry : angle 0.60741 (44379) SS BOND : bond 0.00243 ( 54) SS BOND : angle 1.13970 ( 108) hydrogen bonds : bond 0.04246 ( 1317) hydrogen bonds : angle 5.50624 ( 3681) link_BETA1-4 : bond 0.00437 ( 18) link_BETA1-4 : angle 1.40015 ( 54) link_NAG-ASN : bond 0.00221 ( 45) link_NAG-ASN : angle 1.83104 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 349 time to evaluate : 1.410 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: A 140 PHE cc_start: 0.7932 (p90) cc_final: 0.7601 (p90) REVERT: A 177 MET cc_start: 0.6179 (mmm) cc_final: 0.5144 (mmt) REVERT: A 223 LEU cc_start: 0.8207 (mt) cc_final: 0.7653 (tp) REVERT: A 269 TYR cc_start: 0.7086 (m-80) cc_final: 0.6827 (m-80) REVERT: A 289 VAL cc_start: 0.8853 (t) cc_final: 0.8491 (p) REVERT: A 402 ILE cc_start: 0.7632 (pt) cc_final: 0.7379 (pt) REVERT: A 473 TYR cc_start: 0.8290 (m-10) cc_final: 0.7680 (m-10) REVERT: A 495 TYR cc_start: 0.6469 (m-80) cc_final: 0.5597 (m-80) REVERT: A 501 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7854 (p0) REVERT: A 762 GLN cc_start: 0.9049 (tt0) cc_final: 0.8524 (tm-30) REVERT: A 968 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8740 (t) REVERT: H 34 MET cc_start: 0.6930 (ptp) cc_final: 0.6584 (ptp) REVERT: H 72 ASP cc_start: 0.7584 (t0) cc_final: 0.6541 (p0) REVERT: H 100 ASP cc_start: 0.8799 (t0) cc_final: 0.8504 (t0) REVERT: L 4 MET cc_start: 0.7930 (tpp) cc_final: 0.7440 (tpt) REVERT: L 35 TRP cc_start: 0.6407 (m100) cc_final: 0.6034 (m100) REVERT: L 42 GLN cc_start: 0.9077 (mt0) cc_final: 0.8740 (mp10) REVERT: L 50 GLN cc_start: 0.9455 (mp10) cc_final: 0.8702 (mp10) REVERT: L 74 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8481 (mttt) REVERT: L 83 VAL cc_start: 0.8763 (m) cc_final: 0.8454 (t) REVERT: L 89 MET cc_start: 0.5438 (ttp) cc_final: 0.5073 (tmm) REVERT: B 138 ASP cc_start: 0.7790 (m-30) cc_final: 0.7430 (p0) REVERT: B 177 MET cc_start: 0.5992 (mmt) cc_final: 0.5596 (mmt) REVERT: B 223 LEU cc_start: 0.8397 (mt) cc_final: 0.7750 (tp) REVERT: B 289 VAL cc_start: 0.8904 (t) cc_final: 0.8627 (p) REVERT: B 473 TYR cc_start: 0.7953 (m-10) cc_final: 0.7491 (m-10) REVERT: B 990 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7694 (tm-30) REVERT: D 38 ARG cc_start: 0.8505 (ptt180) cc_final: 0.8230 (ptt-90) REVERT: D 72 ASP cc_start: 0.7373 (t0) cc_final: 0.6310 (p0) REVERT: D 85 GLU cc_start: 0.7537 (pm20) cc_final: 0.7263 (mp0) REVERT: F 54 ARG cc_start: 0.8781 (ttt90) cc_final: 0.8088 (tpt-90) REVERT: F 75 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6770 (tp) REVERT: F 93 HIS cc_start: 0.8657 (m90) cc_final: 0.8216 (m-70) REVERT: C 138 ASP cc_start: 0.7631 (m-30) cc_final: 0.7040 (p0) REVERT: C 140 PHE cc_start: 0.8058 (p90) cc_final: 0.7136 (p90) REVERT: C 177 MET cc_start: 0.5444 (mmt) cc_final: 0.5205 (mmt) REVERT: C 223 LEU cc_start: 0.8201 (mt) cc_final: 0.7696 (tp) REVERT: C 289 VAL cc_start: 0.8897 (t) cc_final: 0.8579 (p) REVERT: C 473 TYR cc_start: 0.8158 (m-10) cc_final: 0.7683 (m-10) REVERT: C 752 LEU cc_start: 0.8710 (mt) cc_final: 0.8263 (tp) REVERT: C 869 MET cc_start: 0.9172 (mtt) cc_final: 0.8791 (mtt) REVERT: E 3 GLN cc_start: 0.9121 (tp40) cc_final: 0.8914 (tp-100) REVERT: E 72 ASP cc_start: 0.7088 (t0) cc_final: 0.6632 (t0) REVERT: E 75 LYS cc_start: 0.9137 (mmmt) cc_final: 0.8819 (mmmt) REVERT: E 82 LEU cc_start: 0.7912 (mt) cc_final: 0.7622 (mp) REVERT: E 100 ASP cc_start: 0.8480 (t0) cc_final: 0.8186 (t0) REVERT: G 4 MET cc_start: 0.8158 (tpp) cc_final: 0.7747 (tpt) REVERT: G 53 ASN cc_start: 0.9086 (t0) cc_final: 0.8841 (t0) REVERT: G 93 HIS cc_start: 0.8804 (m90) cc_final: 0.8447 (m-70) outliers start: 83 outliers final: 52 residues processed: 409 average time/residue: 0.2165 time to fit residues: 143.1689 Evaluate side-chains 374 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 319 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 501 ASN Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 CYS Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain G residue 21 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 363 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.0470 chunk 27 optimal weight: 0.8980 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 501 ASN A 836 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 501 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 856 ASN C1142 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.099158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.073703 restraints weight = 94720.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.076304 restraints weight = 49431.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.078009 restraints weight = 32033.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.079206 restraints weight = 23883.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.079915 restraints weight = 19463.834| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32754 Z= 0.158 Angle : 0.620 9.680 44676 Z= 0.314 Chirality : 0.044 0.244 5151 Planarity : 0.004 0.040 5682 Dihedral : 5.321 54.771 5628 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer: Outliers : 2.58 % Allowed : 11.95 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.13), residues: 3948 helix: 2.69 (0.20), residues: 654 sheet: 0.61 (0.16), residues: 912 loop : -0.66 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.030 0.002 TYR F 49 PHE 0.061 0.002 PHE A 497 TRP 0.011 0.001 TRP C 104 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00360 (32637) covalent geometry : angle 0.61028 (44379) SS BOND : bond 0.00313 ( 54) SS BOND : angle 1.11172 ( 108) hydrogen bonds : bond 0.04311 ( 1317) hydrogen bonds : angle 5.46073 ( 3681) link_BETA1-4 : bond 0.00443 ( 18) link_BETA1-4 : angle 1.34915 ( 54) link_NAG-ASN : bond 0.00222 ( 45) link_NAG-ASN : angle 1.77211 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 333 time to evaluate : 1.323 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: A 138 ASP cc_start: 0.7828 (m-30) cc_final: 0.7018 (p0) REVERT: A 140 PHE cc_start: 0.7958 (p90) cc_final: 0.7656 (p90) REVERT: A 223 LEU cc_start: 0.8266 (mt) cc_final: 0.7730 (tp) REVERT: A 269 TYR cc_start: 0.7190 (m-80) cc_final: 0.6889 (m-80) REVERT: A 289 VAL cc_start: 0.8871 (t) cc_final: 0.8528 (p) REVERT: A 473 TYR cc_start: 0.8317 (m-10) cc_final: 0.7692 (m-10) REVERT: A 486 PHE cc_start: 0.7712 (t80) cc_final: 0.7477 (t80) REVERT: A 495 TYR cc_start: 0.6564 (m-80) cc_final: 0.5866 (m-80) REVERT: A 501 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7760 (p0) REVERT: A 762 GLN cc_start: 0.9042 (tt0) cc_final: 0.8521 (tm-30) REVERT: A 869 MET cc_start: 0.9001 (mtm) cc_final: 0.8703 (mtt) REVERT: H 34 MET cc_start: 0.7058 (ptp) cc_final: 0.6704 (ptp) REVERT: H 72 ASP cc_start: 0.7594 (t0) cc_final: 0.6552 (p0) REVERT: H 77 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7523 (m) REVERT: H 100 ASP cc_start: 0.8744 (t0) cc_final: 0.8449 (t0) REVERT: L 4 MET cc_start: 0.7835 (tpp) cc_final: 0.7558 (tpp) REVERT: L 35 TRP cc_start: 0.6467 (m100) cc_final: 0.6031 (m100) REVERT: L 42 GLN cc_start: 0.9068 (mt0) cc_final: 0.8745 (mp10) REVERT: L 74 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8557 (mttt) REVERT: L 75 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6513 (tp) REVERT: L 89 MET cc_start: 0.5448 (ttp) cc_final: 0.5129 (tmm) REVERT: L 105 GLU cc_start: 0.6963 (tp30) cc_final: 0.6753 (mp0) REVERT: B 138 ASP cc_start: 0.7813 (m-30) cc_final: 0.7505 (p0) REVERT: B 177 MET cc_start: 0.5971 (mmt) cc_final: 0.5568 (mmt) REVERT: B 223 LEU cc_start: 0.8409 (mt) cc_final: 0.7758 (tp) REVERT: B 289 VAL cc_start: 0.8906 (t) cc_final: 0.8606 (p) REVERT: B 473 TYR cc_start: 0.8015 (m-10) cc_final: 0.7502 (m-10) REVERT: B 486 PHE cc_start: 0.7450 (t80) cc_final: 0.7165 (t80) REVERT: B 869 MET cc_start: 0.8998 (mtt) cc_final: 0.8796 (mtt) REVERT: B 968 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8959 (t) REVERT: B 990 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7692 (tm-30) REVERT: D 72 ASP cc_start: 0.7376 (t0) cc_final: 0.6256 (p0) REVERT: F 50 GLN cc_start: 0.9394 (mp10) cc_final: 0.8856 (mp10) REVERT: F 54 ARG cc_start: 0.8772 (ttt90) cc_final: 0.7926 (tpt-90) REVERT: F 75 ILE cc_start: 0.6399 (OUTLIER) cc_final: 0.6102 (mt) REVERT: F 83 VAL cc_start: 0.8722 (m) cc_final: 0.8454 (t) REVERT: F 93 HIS cc_start: 0.8724 (m90) cc_final: 0.8260 (m-70) REVERT: C 138 ASP cc_start: 0.7695 (m-30) cc_final: 0.7207 (p0) REVERT: C 140 PHE cc_start: 0.8101 (p90) cc_final: 0.7158 (p90) REVERT: C 177 MET cc_start: 0.5537 (mmt) cc_final: 0.5235 (mmt) REVERT: C 223 LEU cc_start: 0.8231 (mt) cc_final: 0.7778 (tp) REVERT: C 289 VAL cc_start: 0.8935 (t) cc_final: 0.8630 (p) REVERT: C 473 TYR cc_start: 0.8184 (m-10) cc_final: 0.7687 (m-10) REVERT: C 486 PHE cc_start: 0.7922 (t80) cc_final: 0.7577 (t80) REVERT: C 869 MET cc_start: 0.9180 (mtt) cc_final: 0.8792 (mtt) REVERT: E 3 GLN cc_start: 0.9320 (tp40) cc_final: 0.9046 (tp-100) REVERT: E 72 ASP cc_start: 0.7072 (t0) cc_final: 0.6625 (t0) REVERT: E 75 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8868 (mmmt) REVERT: E 82 LEU cc_start: 0.7783 (mt) cc_final: 0.7499 (mp) REVERT: E 100 ASP cc_start: 0.8370 (t0) cc_final: 0.8009 (t0) REVERT: G 4 MET cc_start: 0.8183 (tpp) cc_final: 0.7803 (tpt) REVERT: G 50 GLN cc_start: 0.9159 (mp10) cc_final: 0.8640 (mp10) REVERT: G 61 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7655 (ptm160) REVERT: G 75 ILE cc_start: 0.7378 (mt) cc_final: 0.7171 (mp) REVERT: G 77 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8414 (ttp-110) REVERT: G 83 VAL cc_start: 0.9023 (m) cc_final: 0.8775 (t) REVERT: G 89 MET cc_start: 0.5675 (ttp) cc_final: 0.5380 (tmm) REVERT: G 93 HIS cc_start: 0.8835 (m90) cc_final: 0.8486 (m-70) outliers start: 89 outliers final: 66 residues processed: 397 average time/residue: 0.2167 time to fit residues: 138.3401 Evaluate side-chains 374 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 303 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 14 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain G residue 21 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 317 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 234 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 291 optimal weight: 0.9990 chunk 392 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 309 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.099367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073746 restraints weight = 97058.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.076312 restraints weight = 52050.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.078075 restraints weight = 34200.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.079227 restraints weight = 25605.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.080005 restraints weight = 21019.804| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32754 Z= 0.143 Angle : 0.616 9.678 44676 Z= 0.311 Chirality : 0.044 0.243 5151 Planarity : 0.004 0.040 5682 Dihedral : 5.341 55.127 5628 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.31 % Allowed : 12.70 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.13), residues: 3948 helix: 2.70 (0.20), residues: 654 sheet: 0.60 (0.16), residues: 906 loop : -0.69 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 38 TYR 0.030 0.001 TYR F 49 PHE 0.062 0.002 PHE B 497 TRP 0.012 0.001 TRP G 35 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00326 (32637) covalent geometry : angle 0.60750 (44379) SS BOND : bond 0.00275 ( 54) SS BOND : angle 1.06085 ( 108) hydrogen bonds : bond 0.04264 ( 1317) hydrogen bonds : angle 5.39075 ( 3681) link_BETA1-4 : bond 0.00385 ( 18) link_BETA1-4 : angle 1.25148 ( 54) link_NAG-ASN : bond 0.00195 ( 45) link_NAG-ASN : angle 1.66182 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 326 time to evaluate : 1.281 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: A 138 ASP cc_start: 0.7958 (m-30) cc_final: 0.7155 (p0) REVERT: A 140 PHE cc_start: 0.7910 (p90) cc_final: 0.7160 (p90) REVERT: A 177 MET cc_start: 0.6205 (mmt) cc_final: 0.5613 (mmt) REVERT: A 223 LEU cc_start: 0.8371 (mt) cc_final: 0.7916 (tp) REVERT: A 269 TYR cc_start: 0.7170 (m-80) cc_final: 0.6865 (m-80) REVERT: A 289 VAL cc_start: 0.8855 (t) cc_final: 0.8494 (p) REVERT: A 473 TYR cc_start: 0.8284 (m-10) cc_final: 0.7666 (m-10) REVERT: A 486 PHE cc_start: 0.7733 (t80) cc_final: 0.7478 (t80) REVERT: A 501 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7928 (p0) REVERT: A 869 MET cc_start: 0.8986 (mtm) cc_final: 0.8645 (mtt) REVERT: H 34 MET cc_start: 0.7200 (ptp) cc_final: 0.6845 (ptp) REVERT: H 72 ASP cc_start: 0.7593 (t0) cc_final: 0.6501 (p0) REVERT: H 77 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7511 (m) REVERT: H 100 ASP cc_start: 0.8622 (t0) cc_final: 0.8328 (t0) REVERT: L 35 TRP cc_start: 0.6461 (m100) cc_final: 0.6007 (m100) REVERT: L 89 MET cc_start: 0.5457 (ttp) cc_final: 0.5160 (tmm) REVERT: B 138 ASP cc_start: 0.7828 (m-30) cc_final: 0.7478 (p0) REVERT: B 177 MET cc_start: 0.6032 (mmt) cc_final: 0.5587 (mmt) REVERT: B 223 LEU cc_start: 0.8420 (mt) cc_final: 0.7767 (tp) REVERT: B 289 VAL cc_start: 0.8932 (t) cc_final: 0.8646 (p) REVERT: B 473 TYR cc_start: 0.8035 (m-10) cc_final: 0.7461 (m-10) REVERT: B 486 PHE cc_start: 0.7546 (t80) cc_final: 0.7217 (t80) REVERT: B 968 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8970 (t) REVERT: B 990 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7655 (tm-30) REVERT: D 34 MET cc_start: 0.7224 (ptp) cc_final: 0.6425 (pmm) REVERT: D 72 ASP cc_start: 0.7361 (t0) cc_final: 0.6273 (p0) REVERT: F 4 MET cc_start: 0.8046 (tpt) cc_final: 0.7598 (tpt) REVERT: F 54 ARG cc_start: 0.8396 (ttt90) cc_final: 0.7928 (tpt-90) REVERT: F 75 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6640 (mt) REVERT: F 83 VAL cc_start: 0.8693 (m) cc_final: 0.8390 (t) REVERT: F 93 HIS cc_start: 0.8708 (m90) cc_final: 0.8280 (m-70) REVERT: C 138 ASP cc_start: 0.7717 (m-30) cc_final: 0.7090 (p0) REVERT: C 140 PHE cc_start: 0.8128 (p90) cc_final: 0.7139 (p90) REVERT: C 177 MET cc_start: 0.5593 (mmt) cc_final: 0.5276 (mmt) REVERT: C 223 LEU cc_start: 0.8315 (mt) cc_final: 0.7906 (tp) REVERT: C 289 VAL cc_start: 0.8916 (t) cc_final: 0.8595 (p) REVERT: C 473 TYR cc_start: 0.8244 (m-10) cc_final: 0.7677 (m-10) REVERT: C 486 PHE cc_start: 0.7971 (t80) cc_final: 0.7607 (t80) REVERT: C 869 MET cc_start: 0.9170 (mtt) cc_final: 0.8777 (mtt) REVERT: E 3 GLN cc_start: 0.9336 (tp40) cc_final: 0.9059 (tp-100) REVERT: E 72 ASP cc_start: 0.7130 (t0) cc_final: 0.6677 (t0) REVERT: E 75 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8896 (mmmt) REVERT: E 82 LEU cc_start: 0.7787 (mt) cc_final: 0.7520 (mp) REVERT: E 100 ASP cc_start: 0.8372 (t0) cc_final: 0.8022 (t0) REVERT: G 4 MET cc_start: 0.8195 (tpp) cc_final: 0.7855 (tpt) REVERT: G 75 ILE cc_start: 0.7569 (mt) cc_final: 0.7268 (tp) REVERT: G 83 VAL cc_start: 0.9000 (m) cc_final: 0.8620 (t) REVERT: G 89 MET cc_start: 0.5750 (ttp) cc_final: 0.5518 (tmm) REVERT: G 93 HIS cc_start: 0.8797 (m90) cc_final: 0.8465 (m-70) outliers start: 80 outliers final: 67 residues processed: 383 average time/residue: 0.2187 time to fit residues: 135.6903 Evaluate side-chains 372 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 301 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain G residue 21 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 283 optimal weight: 8.9990 chunk 336 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 327 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 391 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN H 81 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.099391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.073711 restraints weight = 95382.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.076288 restraints weight = 51022.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.078019 restraints weight = 33617.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.079159 restraints weight = 25277.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.079845 restraints weight = 20851.133| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32754 Z= 0.126 Angle : 0.611 17.398 44676 Z= 0.306 Chirality : 0.044 0.232 5151 Planarity : 0.004 0.064 5682 Dihedral : 5.325 55.191 5628 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.29 % Allowed : 13.34 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.13), residues: 3948 helix: 2.76 (0.20), residues: 654 sheet: 0.63 (0.16), residues: 936 loop : -0.74 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 77 TYR 0.029 0.001 TYR G 49 PHE 0.048 0.002 PHE B 497 TRP 0.014 0.001 TRP G 35 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00284 (32637) covalent geometry : angle 0.60300 (44379) SS BOND : bond 0.00262 ( 54) SS BOND : angle 0.99474 ( 108) hydrogen bonds : bond 0.04120 ( 1317) hydrogen bonds : angle 5.30948 ( 3681) link_BETA1-4 : bond 0.00402 ( 18) link_BETA1-4 : angle 1.21417 ( 54) link_NAG-ASN : bond 0.00185 ( 45) link_NAG-ASN : angle 1.58926 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 332 time to evaluate : 1.512 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: A 138 ASP cc_start: 0.7969 (m-30) cc_final: 0.7176 (p0) REVERT: A 140 PHE cc_start: 0.7925 (p90) cc_final: 0.7193 (p90) REVERT: A 177 MET cc_start: 0.6317 (mmt) cc_final: 0.5846 (mmt) REVERT: A 223 LEU cc_start: 0.8326 (mt) cc_final: 0.7886 (tp) REVERT: A 269 TYR cc_start: 0.7198 (m-80) cc_final: 0.6910 (m-80) REVERT: A 289 VAL cc_start: 0.8853 (t) cc_final: 0.8506 (p) REVERT: A 473 TYR cc_start: 0.8275 (m-10) cc_final: 0.7655 (m-10) REVERT: A 486 PHE cc_start: 0.7692 (t80) cc_final: 0.7477 (t80) REVERT: A 501 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7963 (p0) REVERT: A 869 MET cc_start: 0.8969 (mtm) cc_final: 0.8755 (mtt) REVERT: A 968 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8796 (t) REVERT: H 34 MET cc_start: 0.7225 (ptp) cc_final: 0.6901 (ptp) REVERT: H 72 ASP cc_start: 0.7666 (t0) cc_final: 0.6526 (p0) REVERT: H 100 ASP cc_start: 0.8567 (t0) cc_final: 0.8362 (t0) REVERT: L 35 TRP cc_start: 0.6412 (m100) cc_final: 0.5941 (m100) REVERT: L 75 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6589 (tp) REVERT: L 89 MET cc_start: 0.5508 (ttp) cc_final: 0.5199 (tmm) REVERT: B 138 ASP cc_start: 0.7837 (m-30) cc_final: 0.7470 (p0) REVERT: B 177 MET cc_start: 0.5943 (mmt) cc_final: 0.5503 (mmt) REVERT: B 223 LEU cc_start: 0.8387 (mt) cc_final: 0.7764 (tp) REVERT: B 289 VAL cc_start: 0.8946 (t) cc_final: 0.8654 (p) REVERT: B 473 TYR cc_start: 0.8055 (m-10) cc_final: 0.7446 (m-10) REVERT: B 486 PHE cc_start: 0.7568 (t80) cc_final: 0.7227 (t80) REVERT: B 731 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8789 (ptt) REVERT: B 990 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7675 (tm-30) REVERT: D 34 MET cc_start: 0.7344 (ptp) cc_final: 0.6603 (pmm) REVERT: D 72 ASP cc_start: 0.7389 (t0) cc_final: 0.6293 (p0) REVERT: F 54 ARG cc_start: 0.8455 (ttt90) cc_final: 0.7974 (tpt-90) REVERT: F 75 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6597 (mt) REVERT: F 93 HIS cc_start: 0.8683 (m90) cc_final: 0.8282 (m-70) REVERT: C 138 ASP cc_start: 0.7714 (m-30) cc_final: 0.7047 (p0) REVERT: C 140 PHE cc_start: 0.8057 (p90) cc_final: 0.7098 (p90) REVERT: C 177 MET cc_start: 0.5475 (mmt) cc_final: 0.5180 (mmt) REVERT: C 223 LEU cc_start: 0.8279 (mt) cc_final: 0.7891 (tp) REVERT: C 289 VAL cc_start: 0.8913 (t) cc_final: 0.8594 (p) REVERT: C 473 TYR cc_start: 0.8220 (m-10) cc_final: 0.7640 (m-10) REVERT: C 486 PHE cc_start: 0.7867 (t80) cc_final: 0.7523 (t80) REVERT: C 571 ASP cc_start: 0.8367 (m-30) cc_final: 0.7922 (t0) REVERT: C 869 MET cc_start: 0.9117 (mtt) cc_final: 0.8729 (mtt) REVERT: E 3 GLN cc_start: 0.9396 (tp40) cc_final: 0.9123 (tp-100) REVERT: E 72 ASP cc_start: 0.7176 (t0) cc_final: 0.6725 (t0) REVERT: E 75 LYS cc_start: 0.9134 (mmmt) cc_final: 0.8919 (mmmt) REVERT: E 82 LEU cc_start: 0.7754 (mt) cc_final: 0.7510 (mp) REVERT: E 100 ASP cc_start: 0.8300 (t0) cc_final: 0.7977 (t0) REVERT: G 4 MET cc_start: 0.8337 (tpp) cc_final: 0.7909 (tpt) REVERT: G 75 ILE cc_start: 0.7549 (mt) cc_final: 0.7086 (tt) REVERT: G 83 VAL cc_start: 0.8934 (m) cc_final: 0.8713 (t) REVERT: G 93 HIS cc_start: 0.8770 (m90) cc_final: 0.8459 (m-70) outliers start: 79 outliers final: 60 residues processed: 388 average time/residue: 0.2133 time to fit residues: 134.2315 Evaluate side-chains 368 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 303 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain G residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 191 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 231 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.099282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073719 restraints weight = 94520.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076351 restraints weight = 49383.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078116 restraints weight = 32015.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.079249 restraints weight = 23810.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.080076 restraints weight = 19503.428| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32754 Z= 0.128 Angle : 0.618 15.411 44676 Z= 0.310 Chirality : 0.045 0.231 5151 Planarity : 0.004 0.041 5682 Dihedral : 5.341 55.072 5628 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 2.08 % Allowed : 13.83 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.13), residues: 3948 helix: 2.77 (0.20), residues: 657 sheet: 0.60 (0.16), residues: 939 loop : -0.75 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.026 0.001 TYR A 495 PHE 0.040 0.002 PHE B 497 TRP 0.016 0.001 TRP G 35 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00291 (32637) covalent geometry : angle 0.61059 (44379) SS BOND : bond 0.00244 ( 54) SS BOND : angle 0.97640 ( 108) hydrogen bonds : bond 0.04073 ( 1317) hydrogen bonds : angle 5.25407 ( 3681) link_BETA1-4 : bond 0.00397 ( 18) link_BETA1-4 : angle 1.17899 ( 54) link_NAG-ASN : bond 0.00176 ( 45) link_NAG-ASN : angle 1.54954 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 330 time to evaluate : 1.196 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: A 138 ASP cc_start: 0.8054 (m-30) cc_final: 0.7268 (p0) REVERT: A 140 PHE cc_start: 0.7965 (p90) cc_final: 0.7304 (p90) REVERT: A 177 MET cc_start: 0.6307 (mmt) cc_final: 0.5692 (mmt) REVERT: A 223 LEU cc_start: 0.8345 (mt) cc_final: 0.7979 (mt) REVERT: A 269 TYR cc_start: 0.7199 (m-80) cc_final: 0.6903 (m-80) REVERT: A 289 VAL cc_start: 0.8843 (t) cc_final: 0.8474 (p) REVERT: A 473 TYR cc_start: 0.8294 (m-10) cc_final: 0.7720 (m-10) REVERT: A 486 PHE cc_start: 0.7714 (t80) cc_final: 0.7497 (t80) REVERT: A 501 ASN cc_start: 0.8199 (OUTLIER) cc_final: 0.7894 (p0) REVERT: A 869 MET cc_start: 0.9023 (mtm) cc_final: 0.8739 (mtt) REVERT: A 968 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8756 (t) REVERT: H 34 MET cc_start: 0.7231 (ptp) cc_final: 0.6869 (ptp) REVERT: H 72 ASP cc_start: 0.7600 (t0) cc_final: 0.6464 (p0) REVERT: H 77 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7557 (m) REVERT: L 35 TRP cc_start: 0.6427 (m100) cc_final: 0.6049 (m100) REVERT: L 60 ASP cc_start: 0.8700 (p0) cc_final: 0.8140 (t70) REVERT: L 75 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6784 (tp) REVERT: L 89 MET cc_start: 0.5477 (ttp) cc_final: 0.5204 (tmm) REVERT: B 138 ASP cc_start: 0.7873 (m-30) cc_final: 0.7340 (p0) REVERT: B 177 MET cc_start: 0.5941 (mmt) cc_final: 0.5510 (mmt) REVERT: B 223 LEU cc_start: 0.8368 (mt) cc_final: 0.7729 (tp) REVERT: B 289 VAL cc_start: 0.8934 (t) cc_final: 0.8614 (p) REVERT: B 473 TYR cc_start: 0.8071 (m-10) cc_final: 0.7468 (m-10) REVERT: B 486 PHE cc_start: 0.7558 (t80) cc_final: 0.7193 (t80) REVERT: B 731 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8826 (ptt) REVERT: B 990 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7624 (tm-30) REVERT: D 34 MET cc_start: 0.7330 (ptp) cc_final: 0.6605 (pmm) REVERT: D 72 ASP cc_start: 0.7368 (t0) cc_final: 0.6309 (p0) REVERT: D 77 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7715 (m) REVERT: D 96 THR cc_start: 0.9269 (t) cc_final: 0.9051 (m) REVERT: F 35 TRP cc_start: 0.6661 (m100) cc_final: 0.6076 (m100) REVERT: F 54 ARG cc_start: 0.8490 (ttt90) cc_final: 0.7989 (tpt-90) REVERT: F 75 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6618 (mt) REVERT: F 89 MET cc_start: 0.5749 (tmm) cc_final: 0.5350 (tmm) REVERT: F 93 HIS cc_start: 0.8709 (m90) cc_final: 0.8295 (m-70) REVERT: F 103 LYS cc_start: 0.9107 (mmmt) cc_final: 0.8580 (mmtm) REVERT: F 105 GLU cc_start: 0.8306 (mp0) cc_final: 0.7966 (tp30) REVERT: C 138 ASP cc_start: 0.7742 (m-30) cc_final: 0.7076 (p0) REVERT: C 140 PHE cc_start: 0.8072 (p90) cc_final: 0.7182 (p90) REVERT: C 177 MET cc_start: 0.5449 (mmt) cc_final: 0.5163 (mmt) REVERT: C 223 LEU cc_start: 0.8329 (mt) cc_final: 0.7911 (tp) REVERT: C 289 VAL cc_start: 0.8890 (t) cc_final: 0.8561 (p) REVERT: C 473 TYR cc_start: 0.8207 (m-10) cc_final: 0.7619 (m-10) REVERT: C 486 PHE cc_start: 0.7886 (t80) cc_final: 0.7593 (t80) REVERT: C 571 ASP cc_start: 0.8345 (m-30) cc_final: 0.7901 (t0) REVERT: C 731 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8716 (ptt) REVERT: C 869 MET cc_start: 0.9120 (mtt) cc_final: 0.8724 (mtt) REVERT: E 3 GLN cc_start: 0.9415 (tp40) cc_final: 0.9019 (tp-100) REVERT: E 72 ASP cc_start: 0.7121 (t0) cc_final: 0.6696 (t0) REVERT: E 75 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8909 (mmmt) REVERT: E 82 LEU cc_start: 0.7766 (mt) cc_final: 0.7544 (mp) REVERT: E 100 ASP cc_start: 0.8278 (t0) cc_final: 0.7955 (t0) REVERT: G 4 MET cc_start: 0.8371 (tpp) cc_final: 0.7870 (tpt) REVERT: G 83 VAL cc_start: 0.8903 (m) cc_final: 0.8387 (t) REVERT: G 93 HIS cc_start: 0.8779 (m90) cc_final: 0.8470 (m-70) outliers start: 72 outliers final: 55 residues processed: 380 average time/residue: 0.2159 time to fit residues: 132.6530 Evaluate side-chains 375 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 312 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 95 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 250 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 345 optimal weight: 0.3980 chunk 295 optimal weight: 0.0470 chunk 247 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 290 optimal weight: 0.0010 overall best weight: 0.6888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 762 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1010 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 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 = 0.3916 r_free = 0.3916 target = 0.102492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075909 restraints weight = 96241.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.078644 restraints weight = 49304.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.080466 restraints weight = 31674.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.081679 restraints weight = 23481.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082481 restraints weight = 19149.986| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32754 Z= 0.121 Angle : 0.622 17.323 44676 Z= 0.312 Chirality : 0.045 0.232 5151 Planarity : 0.004 0.071 5682 Dihedral : 5.344 57.299 5628 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 1.74 % Allowed : 14.35 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.13), residues: 3948 helix: 2.63 (0.20), residues: 681 sheet: 0.54 (0.16), residues: 960 loop : -0.70 (0.12), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 24 TYR 0.028 0.001 TYR L 49 PHE 0.035 0.002 PHE B 497 TRP 0.017 0.001 TRP G 35 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00273 (32637) covalent geometry : angle 0.61487 (44379) SS BOND : bond 0.00244 ( 54) SS BOND : angle 1.07431 ( 108) hydrogen bonds : bond 0.04006 ( 1317) hydrogen bonds : angle 5.19819 ( 3681) link_BETA1-4 : bond 0.00422 ( 18) link_BETA1-4 : angle 1.15992 ( 54) link_NAG-ASN : bond 0.00178 ( 45) link_NAG-ASN : angle 1.51315 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7896 Ramachandran restraints generated. 3948 Oldfield, 0 Emsley, 3948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 331 time to evaluate : 1.297 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: A 138 ASP cc_start: 0.8105 (m-30) cc_final: 0.7285 (p0) REVERT: A 140 PHE cc_start: 0.7951 (p90) cc_final: 0.7302 (p90) REVERT: A 177 MET cc_start: 0.6358 (mmt) cc_final: 0.5766 (mmt) REVERT: A 223 LEU cc_start: 0.8370 (mt) cc_final: 0.7866 (tp) REVERT: A 269 TYR cc_start: 0.7162 (m-80) cc_final: 0.6875 (m-80) REVERT: A 289 VAL cc_start: 0.8806 (t) cc_final: 0.8364 (p) REVERT: A 473 TYR cc_start: 0.8288 (m-10) cc_final: 0.7693 (m-10) REVERT: A 486 PHE cc_start: 0.7716 (t80) cc_final: 0.7492 (t80) REVERT: A 501 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7919 (p0) REVERT: A 752 LEU cc_start: 0.8851 (mt) cc_final: 0.8419 (tp) REVERT: A 867 ASP cc_start: 0.8407 (m-30) cc_final: 0.8024 (p0) REVERT: A 869 MET cc_start: 0.9023 (mtm) cc_final: 0.8726 (mtt) REVERT: A 968 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8678 (t) REVERT: H 34 MET cc_start: 0.7207 (ptp) cc_final: 0.6813 (ptp) REVERT: H 64 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8124 (mp0) REVERT: H 72 ASP cc_start: 0.7462 (t0) cc_final: 0.6306 (p0) REVERT: L 35 TRP cc_start: 0.6406 (m100) cc_final: 0.5834 (m100) REVERT: L 89 MET cc_start: 0.5468 (ttp) cc_final: 0.4997 (tmm) REVERT: B 138 ASP cc_start: 0.7887 (m-30) cc_final: 0.7165 (p0) REVERT: B 177 MET cc_start: 0.6072 (mmt) cc_final: 0.5597 (mmt) REVERT: B 223 LEU cc_start: 0.8343 (mt) cc_final: 0.7696 (tp) REVERT: B 289 VAL cc_start: 0.8859 (t) cc_final: 0.8318 (p) REVERT: B 473 TYR cc_start: 0.8076 (m-10) cc_final: 0.7457 (m-10) REVERT: B 486 PHE cc_start: 0.7569 (t80) cc_final: 0.7191 (t80) REVERT: B 731 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8831 (ptt) REVERT: B 990 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7594 (tm-30) REVERT: D 72 ASP cc_start: 0.7363 (t0) cc_final: 0.6294 (p0) REVERT: D 77 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7670 (m) REVERT: D 96 THR cc_start: 0.9253 (t) cc_final: 0.9013 (m) REVERT: F 35 TRP cc_start: 0.6751 (m100) cc_final: 0.6069 (m100) REVERT: F 54 ARG cc_start: 0.8515 (ttt90) cc_final: 0.7972 (tpt-90) REVERT: F 75 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6633 (mt) REVERT: F 89 MET cc_start: 0.5553 (tmm) cc_final: 0.5274 (tmm) REVERT: F 93 HIS cc_start: 0.8766 (m90) cc_final: 0.8335 (m-70) REVERT: F 103 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8687 (mmtt) REVERT: F 105 GLU cc_start: 0.8264 (mp0) cc_final: 0.7972 (tp30) REVERT: C 138 ASP cc_start: 0.7731 (m-30) cc_final: 0.7167 (p0) REVERT: C 140 PHE cc_start: 0.8045 (p90) cc_final: 0.7143 (p90) REVERT: C 177 MET cc_start: 0.5547 (mmt) cc_final: 0.5216 (mmt) REVERT: C 223 LEU cc_start: 0.8333 (mt) cc_final: 0.7909 (tp) REVERT: C 289 VAL cc_start: 0.8889 (t) cc_final: 0.8526 (p) REVERT: C 473 TYR cc_start: 0.8196 (m-10) cc_final: 0.7611 (m-10) REVERT: C 486 PHE cc_start: 0.7909 (t80) cc_final: 0.7609 (t80) REVERT: C 571 ASP cc_start: 0.8365 (m-30) cc_final: 0.7917 (t0) REVERT: C 731 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8709 (ptt) REVERT: C 869 MET cc_start: 0.9128 (mtt) cc_final: 0.8720 (mtt) REVERT: E 3 GLN cc_start: 0.9421 (tp40) cc_final: 0.9142 (tp-100) REVERT: E 72 ASP cc_start: 0.7073 (t0) cc_final: 0.6660 (t0) REVERT: E 75 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8916 (mmmt) REVERT: E 82 LEU cc_start: 0.7653 (mt) cc_final: 0.7433 (mp) REVERT: E 100 ASP cc_start: 0.8337 (t0) cc_final: 0.8036 (t0) REVERT: G 4 MET cc_start: 0.8392 (tpp) cc_final: 0.7953 (tpt) REVERT: G 83 VAL cc_start: 0.8799 (m) cc_final: 0.8460 (t) REVERT: G 93 HIS cc_start: 0.8797 (m90) cc_final: 0.8464 (m-70) REVERT: G 105 GLU cc_start: 0.5206 (tp30) cc_final: 0.4988 (tp30) outliers start: 60 outliers final: 47 residues processed: 371 average time/residue: 0.2135 time to fit residues: 128.6605 Evaluate side-chains 354 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain E residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 183 optimal weight: 4.9990 chunk 349 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 395 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 380 optimal weight: 0.5980 chunk 389 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.102370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075868 restraints weight = 99712.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.078579 restraints weight = 52108.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.080399 restraints weight = 33858.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081613 restraints weight = 25254.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.082325 restraints weight = 20669.335| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32754 Z= 0.126 Angle : 0.625 16.993 44676 Z= 0.314 Chirality : 0.045 0.247 5151 Planarity : 0.004 0.065 5682 Dihedral : 5.365 58.925 5628 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.95 % Favored : 95.97 % Rotamer: Outliers : 1.79 % Allowed : 14.53 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.13), residues: 3948 helix: 2.63 (0.21), residues: 675 sheet: 0.54 (0.16), residues: 960 loop : -0.70 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 24 TYR 0.025 0.001 TYR L 49 PHE 0.034 0.002 PHE C 201 TRP 0.017 0.001 TRP G 35 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00286 (32637) covalent geometry : angle 0.61664 (44379) SS BOND : bond 0.00314 ( 54) SS BOND : angle 1.32457 ( 108) hydrogen bonds : bond 0.03984 ( 1317) hydrogen bonds : angle 5.18648 ( 3681) link_BETA1-4 : bond 0.00395 ( 18) link_BETA1-4 : angle 1.14294 ( 54) link_NAG-ASN : bond 0.00172 ( 45) link_NAG-ASN : angle 1.49236 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6276.74 seconds wall clock time: 109 minutes 21.16 seconds (6561.16 seconds total)