Starting phenix.real_space_refine on Fri Jun 27 21:51:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aru_43794/06_2025/9aru_43794.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aru_43794/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9aru_43794/06_2025/9aru_43794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aru_43794/06_2025/9aru_43794.map" model { file = "/net/cci-nas-00/data/ceres_data/9aru_43794/06_2025/9aru_43794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aru_43794/06_2025/9aru_43794.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.46, per 1000 atoms: 0.55 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: 7.37 Conformation dependent library (CDL) restraints added in 3.9 seconds 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: 5.23 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: 18.44 Time building geometry restraints manager: 8.89 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: 0.02 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.230 Check model and map are aligned: 0.250 Set scattering table: 0.290 Process input model: 77.690 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.270 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP D 36 HIS 0.010 0.002 HIS C1064 PHE 0.021 0.003 PHE A 133 TYR 0.027 0.003 TYR B 756 ARG 0.007 0.001 ARG B 567 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 45) link_NAG-ASN : angle 1.92717 ( 135) link_BETA1-4 : bond 0.01272 ( 18) link_BETA1-4 : angle 3.49538 ( 54) hydrogen bonds : bond 0.14639 ( 1317) hydrogen bonds : angle 7.52950 ( 3681) SS BOND : bond 0.00737 ( 54) SS BOND : angle 2.35853 ( 108) covalent geometry : bond 0.00568 (32637) covalent geometry : angle 1.04468 (44379) *********************** 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 : 3.235 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: 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: 0.7696 (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: 0.6500 (m-80) REVERT: A 276 LEU cc_start: 0.8920 (tp) cc_final: 0.8671 (tt) REVERT: A 289 VAL cc_start: 0.8641 (t) cc_final: 0.8229 (p) REVERT: A 353 TRP cc_start: 0.8597 (p-90) cc_final: 0.7732 (p-90) REVERT: A 400 PHE cc_start: 0.7540 (p90) cc_final: 0.7306 (p90) REVERT: A 402 ILE cc_start: 0.7641 (pt) cc_final: 0.6984 (pt) REVERT: A 495 TYR cc_start: 0.6187 (m-80) cc_final: 0.5826 (m-80) REVERT: A 562 PHE cc_start: 0.7111 (p90) cc_final: 0.6826 (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: 0.8732 (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: 0.8158 (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: 0.8240 (mp10) REVERT: H 34 MET cc_start: 0.6372 (mtp) cc_final: 0.6011 (mtp) REVERT: H 59 TYR cc_start: 0.8151 (m-80) cc_final: 0.7322 (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 35 TRP cc_start: 0.6609 (m100) cc_final: 0.6204 (m100) REVERT: L 104 LEU cc_start: 0.9139 (tt) cc_final: 0.8893 (tt) REVERT: B 140 PHE cc_start: 0.7936 (p90) cc_final: 0.7665 (p90) REVERT: B 177 MET cc_start: 0.5734 (mmt) cc_final: 0.5480 (mmm) REVERT: B 223 LEU cc_start: 0.8161 (mt) cc_final: 0.7737 (tp) REVERT: B 267 VAL cc_start: 0.7869 (t) cc_final: 0.6938 (t) REVERT: B 289 VAL cc_start: 0.8609 (t) cc_final: 0.8205 (p) REVERT: B 353 TRP cc_start: 0.8670 (p-90) cc_final: 0.7602 (p-90) REVERT: B 392 PHE cc_start: 0.7658 (m-80) cc_final: 0.7132 (m-80) REVERT: B 402 ILE cc_start: 0.7755 (pt) cc_final: 0.7397 (pt) REVERT: B 562 PHE cc_start: 0.7563 (p90) cc_final: 0.7089 (p90) REVERT: B 785 VAL cc_start: 0.9505 (t) cc_final: 0.8917 (p) REVERT: B 824 ASN cc_start: 0.8707 (m-40) cc_final: 0.8458 (t0) REVERT: B 945 LEU cc_start: 0.8635 (mt) cc_final: 0.8381 (mt) REVERT: B 990 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7630 (tm-30) REVERT: B 1011 GLN cc_start: 0.8678 (tp40) cc_final: 0.8055 (tp40) REVERT: D 59 TYR cc_start: 0.8139 (m-80) cc_final: 0.7634 (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: 0.6846 (tpt) REVERT: F 35 TRP cc_start: 0.6683 (m100) cc_final: 0.6434 (m100) REVERT: F 93 HIS cc_start: 0.8501 (m90) cc_final: 0.8005 (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: 0.5190 (mmm) REVERT: C 223 LEU cc_start: 0.8170 (mt) cc_final: 0.7953 (mp) REVERT: C 240 THR cc_start: 0.8815 (p) cc_final: 0.8592 (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: 0.8180 (p) REVERT: C 353 TRP cc_start: 0.8713 (p-90) cc_final: 0.7822 (p-90) REVERT: C 400 PHE cc_start: 0.7167 (p90) cc_final: 0.6952 (p90) REVERT: C 402 ILE cc_start: 0.7605 (pt) cc_final: 0.7032 (pt) REVERT: C 434 ILE cc_start: 0.8166 (mt) cc_final: 0.7935 (mp) REVERT: C 495 TYR cc_start: 0.6655 (m-80) cc_final: 0.6013 (m-80) REVERT: C 562 PHE cc_start: 0.7327 (p90) cc_final: 0.7076 (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: 0.8286 (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: 0.6894 (t80) REVERT: E 72 ASP cc_start: 0.7055 (t0) cc_final: 0.6819 (t0) REVERT: G 4 MET cc_start: 0.7883 (tpp) cc_final: 0.7200 (tpt) REVERT: G 93 HIS cc_start: 0.8541 (m90) cc_final: 0.8256 (m90) outliers start: 3 outliers final: 0 residues processed: 843 average time/residue: 0.4872 time to fit residues: 631.2570 Evaluate side-chains 408 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 160 optimal weight: 0.0970 chunk 310 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 chunk 231 optimal weight: 3.9990 chunk 359 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 L 30 ASN L 37 GLN ** 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 53 ASN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.105310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.079566 restraints weight = 94574.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.082450 restraints weight = 46930.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.084407 restraints weight = 29396.235| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2511 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= 0.155 Angle : 0.708 13.726 44676 Z= 0.367 Chirality : 0.046 0.337 5151 Planarity : 0.005 0.093 5682 Dihedral : 5.466 54.733 5628 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.74 % Allowed : 8.54 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 3948 helix: 2.52 (0.19), residues: 672 sheet: 0.82 (0.15), residues: 939 loop : -0.08 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 104 HIS 0.006 0.001 HIS B 519 PHE 0.028 0.002 PHE D 67 TYR 0.024 0.002 TYR A 660 ARG 0.007 0.001 ARG G 39 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 45) link_NAG-ASN : angle 2.78081 ( 135) link_BETA1-4 : bond 0.00534 ( 18) link_BETA1-4 : angle 1.89209 ( 54) hydrogen bonds : bond 0.05232 ( 1317) hydrogen bonds : angle 6.20685 ( 3681) SS BOND : bond 0.00372 ( 54) SS BOND : angle 1.74888 ( 108) covalent geometry : bond 0.00334 (32637) covalent geometry : angle 0.68557 (44379) *********************** 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 546 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 486 time to evaluate : 3.345 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 135 PHE cc_start: 0.7834 (m-80) cc_final: 0.7623 (m-80) REVERT: A 177 MET cc_start: 0.6468 (mmm) cc_final: 0.6200 (mmm) REVERT: A 200 TYR cc_start: 0.8479 (m-80) cc_final: 0.8039 (m-80) REVERT: A 223 LEU cc_start: 0.7987 (mt) cc_final: 0.7710 (mp) REVERT: A 237 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7402 (mtm110) REVERT: A 269 TYR cc_start: 0.6907 (m-80) cc_final: 0.6621 (m-80) REVERT: A 276 LEU cc_start: 0.8988 (tp) cc_final: 0.8778 (tt) REVERT: A 289 VAL cc_start: 0.8830 (t) cc_final: 0.8526 (p) REVERT: A 402 ILE cc_start: 0.7680 (pt) cc_final: 0.7320 (pt) REVERT: A 473 TYR cc_start: 0.8300 (m-10) cc_final: 0.7998 (m-10) REVERT: A 495 TYR cc_start: 0.6218 (m-80) cc_final: 0.5882 (m-80) REVERT: A 759 PHE cc_start: 0.8460 (m-10) cc_final: 0.8016 (m-80) REVERT: A 869 MET cc_start: 0.9064 (mtt) cc_final: 0.8860 (mtt) REVERT: A 968 SER cc_start: 0.8965 (OUTLIER) cc_final: 0.8495 (t) REVERT: A 993 ILE cc_start: 0.8913 (mt) cc_final: 0.8697 (tt) REVERT: A 1011 GLN cc_start: 0.8787 (tp40) cc_final: 0.8305 (tp40) REVERT: H 59 TYR cc_start: 0.8084 (m-80) cc_final: 0.7320 (m-10) REVERT: H 72 ASP cc_start: 0.7614 (t0) cc_final: 0.6431 (p0) REVERT: L 4 MET cc_start: 0.8012 (tpp) cc_final: 0.7581 (tpt) REVERT: L 21 ILE cc_start: 0.8585 (mp) cc_final: 0.8246 (tp) REVERT: L 35 TRP cc_start: 0.6374 (m100) cc_final: 0.6077 (m100) REVERT: L 54 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8384 (ttt90) REVERT: L 83 VAL cc_start: 0.9093 (m) cc_final: 0.8847 (t) REVERT: B 104 TRP cc_start: 0.8412 (m-90) cc_final: 0.6839 (m100) REVERT: B 140 PHE cc_start: 0.7860 (p90) cc_final: 0.7651 (p90) REVERT: B 200 TYR cc_start: 0.8592 (m-80) cc_final: 0.8247 (m-80) REVERT: B 223 LEU cc_start: 0.8132 (mt) cc_final: 0.7921 (mp) REVERT: B 289 VAL cc_start: 0.8846 (t) cc_final: 0.8569 (p) REVERT: B 392 PHE cc_start: 0.7694 (m-80) cc_final: 0.7307 (m-80) REVERT: B 402 ILE cc_start: 0.7888 (pt) cc_final: 0.7368 (pt) REVERT: B 434 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7654 (tp) REVERT: B 990 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7711 (tm-30) REVERT: B 1011 GLN cc_start: 0.8849 (tp40) cc_final: 0.8345 (tp40) REVERT: D 59 TYR cc_start: 0.8039 (m-80) cc_final: 0.7402 (m-80) REVERT: D 72 ASP cc_start: 0.7345 (t0) cc_final: 0.6325 (p0) REVERT: F 21 ILE cc_start: 0.9148 (mp) cc_final: 0.8647 (tt) REVERT: F 93 HIS cc_start: 0.8577 (m90) cc_final: 0.8049 (m-70) REVERT: C 140 PHE cc_start: 0.7788 (p90) cc_final: 0.7060 (p90) REVERT: C 223 LEU cc_start: 0.8184 (mt) cc_final: 0.7970 (mp) REVERT: C 269 TYR cc_start: 0.7166 (m-80) cc_final: 0.6185 (m-80) REVERT: C 276 LEU cc_start: 0.9024 (tp) cc_final: 0.8698 (tt) REVERT: C 289 VAL cc_start: 0.8974 (t) cc_final: 0.8612 (p) REVERT: C 402 ILE cc_start: 0.7775 (pt) cc_final: 0.7558 (pt) REVERT: C 473 TYR cc_start: 0.8088 (m-10) cc_final: 0.7800 (m-10) REVERT: C 495 TYR cc_start: 0.6601 (m-80) cc_final: 0.5994 (m-80) REVERT: C 869 MET cc_start: 0.9151 (mtt) cc_final: 0.8730 (mtt) REVERT: C 1011 GLN cc_start: 0.8751 (tp40) cc_final: 0.8359 (tp40) REVERT: E 1 GLN cc_start: 0.8447 (tm130) cc_final: 0.7844 (tm-30) REVERT: E 3 GLN cc_start: 0.9043 (tp40) cc_final: 0.8776 (tp40) REVERT: E 72 ASP cc_start: 0.6995 (t0) cc_final: 0.6653 (t0) REVERT: E 75 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8968 (mmmt) REVERT: E 79 TYR cc_start: 0.6842 (m-80) cc_final: 0.6589 (m-10) REVERT: G 4 MET cc_start: 0.7868 (tpp) cc_final: 0.7385 (tpt) REVERT: G 42 GLN cc_start: 0.9186 (mt0) cc_final: 0.8894 (mp10) REVERT: G 54 ARG cc_start: 0.8719 (ttt90) cc_final: 0.8356 (ttt90) REVERT: G 93 HIS cc_start: 0.8646 (m90) cc_final: 0.8189 (m-70) outliers start: 60 outliers final: 37 residues processed: 520 average time/residue: 0.4948 time to fit residues: 420.1043 Evaluate side-chains 414 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 374 time to evaluate : 3.585 ------------------------------------------------------------------------------- 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 L residue 75 ILE Chi-restraints excluded: chain B residue 120 VAL 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 705 CYS Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 75 ILE 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 G residue 61 ARG Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 213 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 317 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 370 optimal weight: 0.9990 chunk 381 optimal weight: 7.9990 chunk 331 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 105 optimal weight: 0.2980 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.102298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075770 restraints weight = 96875.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.078569 restraints weight = 49004.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.080432 restraints weight = 31348.850| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32754 Z= 0.189 Angle : 0.683 12.125 44676 Z= 0.346 Chirality : 0.045 0.242 5151 Planarity : 0.004 0.052 5682 Dihedral : 5.391 53.496 5628 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.27 % Favored : 96.66 % Rotamer: Outliers : 2.43 % Allowed : 9.52 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.13), residues: 3948 helix: 2.50 (0.20), residues: 675 sheet: 0.76 (0.16), residues: 936 loop : -0.33 (0.12), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.006 0.001 HIS B 519 PHE 0.029 0.002 PHE B 497 TYR 0.042 0.002 TYR F 49 ARG 0.014 0.001 ARG B1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 45) link_NAG-ASN : angle 2.59388 ( 135) link_BETA1-4 : bond 0.00500 ( 18) link_BETA1-4 : angle 1.72291 ( 54) hydrogen bonds : bond 0.04773 ( 1317) hydrogen bonds : angle 5.87702 ( 3681) SS BOND : bond 0.00405 ( 54) SS BOND : angle 1.31606 ( 108) covalent geometry : bond 0.00426 (32637) covalent geometry : angle 0.66460 (44379) *********************** 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 468 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 384 time to evaluate : 3.833 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: A 177 MET cc_start: 0.5857 (mmm) cc_final: 0.5545 (mmm) REVERT: A 200 TYR cc_start: 0.8569 (m-80) cc_final: 0.8262 (m-80) REVERT: A 223 LEU cc_start: 0.8103 (mt) cc_final: 0.7798 (mp) REVERT: A 269 TYR cc_start: 0.7020 (m-80) cc_final: 0.6739 (m-80) REVERT: A 289 VAL cc_start: 0.8852 (t) cc_final: 0.8590 (p) REVERT: A 318 PHE cc_start: 0.7052 (t80) cc_final: 0.6626 (t80) REVERT: A 402 ILE cc_start: 0.7832 (pt) cc_final: 0.7511 (pt) REVERT: A 473 TYR cc_start: 0.8339 (m-10) cc_final: 0.7880 (m-10) REVERT: A 495 TYR cc_start: 0.6380 (m-80) cc_final: 0.5928 (m-80) REVERT: A 869 MET cc_start: 0.9098 (mtt) cc_final: 0.8855 (mtt) REVERT: A 984 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 1011 GLN cc_start: 0.8883 (tp40) cc_final: 0.8436 (tp40) REVERT: H 72 ASP cc_start: 0.7578 (t0) cc_final: 0.6468 (p0) REVERT: H 83 ARG cc_start: 0.7823 (mmt90) cc_final: 0.7398 (mmt90) REVERT: H 100 ASP cc_start: 0.8674 (t0) cc_final: 0.8415 (t0) REVERT: L 4 MET cc_start: 0.7985 (tpp) cc_final: 0.7576 (tpt) REVERT: L 35 TRP cc_start: 0.6399 (m100) cc_final: 0.6181 (m100) REVERT: L 89 MET cc_start: 0.5299 (ttp) cc_final: 0.4964 (tmm) REVERT: B 41 LYS cc_start: 0.8143 (mttp) cc_final: 0.7931 (mttt) REVERT: B 104 TRP cc_start: 0.8473 (m-90) cc_final: 0.8271 (m-90) REVERT: B 138 ASP cc_start: 0.7770 (m-30) cc_final: 0.7470 (p0) REVERT: B 200 TYR cc_start: 0.8509 (m-80) cc_final: 0.8217 (m-80) REVERT: B 223 LEU cc_start: 0.8196 (mt) cc_final: 0.7821 (tp) REVERT: B 289 VAL cc_start: 0.8893 (t) cc_final: 0.8652 (p) REVERT: B 400 PHE cc_start: 0.7783 (p90) cc_final: 0.7570 (p90) REVERT: B 402 ILE cc_start: 0.7946 (pt) cc_final: 0.7671 (pt) REVERT: B 869 MET cc_start: 0.9046 (mtt) cc_final: 0.8789 (mtt) REVERT: B 984 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 990 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7652 (tm-30) REVERT: B 1011 GLN cc_start: 0.8958 (tp40) cc_final: 0.8375 (tp40) REVERT: D 72 ASP cc_start: 0.7456 (t0) cc_final: 0.6266 (p0) REVERT: F 21 ILE cc_start: 0.9074 (mp) cc_final: 0.8614 (tp) REVERT: F 93 HIS cc_start: 0.8622 (m90) cc_final: 0.8088 (m-70) REVERT: C 138 ASP cc_start: 0.7707 (m-30) cc_final: 0.7028 (p0) REVERT: C 140 PHE cc_start: 0.7881 (p90) cc_final: 0.6729 (p90) REVERT: C 177 MET cc_start: 0.5976 (mmt) cc_final: 0.5502 (mmt) REVERT: C 200 TYR cc_start: 0.8469 (m-80) cc_final: 0.8229 (m-80) REVERT: C 223 LEU cc_start: 0.8149 (mt) cc_final: 0.7915 (mp) REVERT: C 269 TYR cc_start: 0.7329 (m-80) cc_final: 0.6315 (m-80) REVERT: C 289 VAL cc_start: 0.8913 (t) cc_final: 0.8642 (p) REVERT: C 393 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7393 (t) REVERT: C 452 LEU cc_start: 0.9035 (mp) cc_final: 0.8720 (mt) REVERT: C 473 TYR cc_start: 0.8109 (m-10) cc_final: 0.7696 (m-10) REVERT: C 495 TYR cc_start: 0.6860 (m-80) cc_final: 0.6098 (m-80) REVERT: C 869 MET cc_start: 0.9182 (mtt) cc_final: 0.8761 (mtt) REVERT: C 984 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8071 (mp) REVERT: C 1011 GLN cc_start: 0.8810 (tp40) cc_final: 0.8555 (tp40) REVERT: E 3 GLN cc_start: 0.9038 (tp40) cc_final: 0.8570 (tp-100) REVERT: E 72 ASP cc_start: 0.6938 (t0) cc_final: 0.5523 (p0) REVERT: E 83 ARG cc_start: 0.8072 (mpt180) cc_final: 0.7814 (mpt180) REVERT: E 100 ASP cc_start: 0.8473 (t0) cc_final: 0.8252 (t0) REVERT: G 4 MET cc_start: 0.8032 (tpp) cc_final: 0.7690 (tpt) REVERT: G 36 PHE cc_start: 0.7037 (m-80) cc_final: 0.6796 (m-80) REVERT: G 42 GLN cc_start: 0.9206 (mt0) cc_final: 0.8875 (mp10) REVERT: G 54 ARG cc_start: 0.8622 (ttt90) cc_final: 0.8128 (tpp-160) REVERT: G 61 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7764 (ttp-170) REVERT: G 93 HIS cc_start: 0.8764 (m90) cc_final: 0.8366 (m-70) REVERT: G 105 GLU cc_start: 0.7746 (tp30) cc_final: 0.7481 (mp0) outliers start: 84 outliers final: 50 residues processed: 445 average time/residue: 0.5034 time to fit residues: 362.9705 Evaluate side-chains 382 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 327 time to evaluate : 3.252 ------------------------------------------------------------------------------- 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 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 705 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 805 ILE 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 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 11 LEU Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 77 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 267 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 705 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 401 VAL 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 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU 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 382 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 372 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 332 optimal weight: 0.7980 chunk 294 optimal weight: 6.9990 chunk 298 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 836 GLN A1048 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B1048 HIS ** 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 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1048 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3925 r_free = 0.3925 target = 0.101875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.076186 restraints weight = 96563.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.078885 restraints weight = 49918.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.080714 restraints weight = 32198.837| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 32754 Z= 0.146 Angle : 0.642 19.226 44676 Z= 0.324 Chirality : 0.045 0.389 5151 Planarity : 0.004 0.083 5682 Dihedral : 5.338 54.651 5628 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 2.43 % Allowed : 9.98 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.13), residues: 3948 helix: 2.70 (0.20), residues: 654 sheet: 0.60 (0.16), residues: 933 loop : -0.48 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.005 0.001 HIS B 519 PHE 0.031 0.002 PHE B 497 TYR 0.039 0.001 TYR L 49 ARG 0.008 0.000 ARG B 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 45) link_NAG-ASN : angle 2.08154 ( 135) link_BETA1-4 : bond 0.00462 ( 18) link_BETA1-4 : angle 1.52492 ( 54) hydrogen bonds : bond 0.04379 ( 1317) hydrogen bonds : angle 5.58935 ( 3681) SS BOND : bond 0.00509 ( 54) SS BOND : angle 1.69887 ( 108) covalent geometry : bond 0.00329 (32637) covalent geometry : angle 0.62567 (44379) *********************** 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 453 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 3.371 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 138 ASP cc_start: 0.7540 (m-30) cc_final: 0.6871 (p0) REVERT: A 140 PHE cc_start: 0.7694 (p90) cc_final: 0.7067 (p90) REVERT: A 177 MET cc_start: 0.5751 (mmm) cc_final: 0.5032 (mmm) REVERT: A 200 TYR cc_start: 0.8631 (m-80) cc_final: 0.8416 (m-80) REVERT: A 223 LEU cc_start: 0.8112 (mt) cc_final: 0.7764 (mp) REVERT: A 269 TYR cc_start: 0.7035 (m-80) cc_final: 0.6773 (m-80) REVERT: A 289 VAL cc_start: 0.8946 (t) cc_final: 0.8545 (p) REVERT: A 318 PHE cc_start: 0.6913 (t80) cc_final: 0.6407 (t80) REVERT: A 402 ILE cc_start: 0.7744 (pt) cc_final: 0.7361 (pt) REVERT: A 473 TYR cc_start: 0.8312 (m-10) cc_final: 0.7763 (m-10) REVERT: A 495 TYR cc_start: 0.6482 (m-80) cc_final: 0.5693 (m-80) REVERT: A 759 PHE cc_start: 0.8596 (m-10) cc_final: 0.8177 (m-80) REVERT: A 762 GLN cc_start: 0.9089 (tt0) cc_final: 0.8635 (tm-30) REVERT: A 869 MET cc_start: 0.9103 (mtt) cc_final: 0.8864 (mtt) REVERT: A 1011 GLN cc_start: 0.8852 (tp40) cc_final: 0.8396 (tp40) REVERT: H 72 ASP cc_start: 0.7564 (t0) cc_final: 0.6509 (p0) REVERT: H 100 ASP cc_start: 0.8716 (t0) cc_final: 0.8474 (t0) REVERT: L 4 MET cc_start: 0.7927 (tpp) cc_final: 0.7509 (tpt) REVERT: L 35 TRP cc_start: 0.6433 (m100) cc_final: 0.6063 (m100) REVERT: L 74 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8385 (mttt) REVERT: L 83 VAL cc_start: 0.8838 (m) cc_final: 0.8079 (t) REVERT: L 89 MET cc_start: 0.5200 (ttp) cc_final: 0.4797 (tmm) REVERT: B 138 ASP cc_start: 0.7797 (m-30) cc_final: 0.7508 (p0) REVERT: B 140 PHE cc_start: 0.7731 (p90) cc_final: 0.7219 (p90) REVERT: B 177 MET cc_start: 0.5963 (mmt) cc_final: 0.5704 (mmt) REVERT: B 223 LEU cc_start: 0.8427 (mt) cc_final: 0.7887 (tp) REVERT: B 289 VAL cc_start: 0.8951 (t) cc_final: 0.8668 (p) REVERT: B 402 ILE cc_start: 0.7911 (pt) cc_final: 0.7675 (pt) REVERT: B 984 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8335 (mp) REVERT: B 990 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7641 (tm-30) REVERT: B 1011 GLN cc_start: 0.8945 (tp40) cc_final: 0.8494 (tp40) REVERT: B 1050 MET cc_start: 0.8720 (ptp) cc_final: 0.8500 (ptt) REVERT: D 38 ARG cc_start: 0.8656 (ptt180) cc_final: 0.8095 (ptt-90) REVERT: D 72 ASP cc_start: 0.7429 (t0) cc_final: 0.6184 (p0) REVERT: F 21 ILE cc_start: 0.9076 (mp) cc_final: 0.8632 (tp) REVERT: F 54 ARG cc_start: 0.8643 (ttt90) cc_final: 0.7917 (tpp-160) REVERT: F 61 ARG cc_start: 0.8210 (ptp-170) cc_final: 0.7590 (ttp-170) REVERT: F 83 VAL cc_start: 0.8847 (m) cc_final: 0.8566 (t) REVERT: F 93 HIS cc_start: 0.8647 (m90) cc_final: 0.8150 (m-70) REVERT: C 138 ASP cc_start: 0.7734 (m-30) cc_final: 0.7069 (p0) REVERT: C 140 PHE cc_start: 0.8019 (p90) cc_final: 0.7207 (p90) REVERT: C 177 MET cc_start: 0.5826 (mmt) cc_final: 0.5425 (mmt) REVERT: C 223 LEU cc_start: 0.8144 (mt) cc_final: 0.7917 (mp) REVERT: C 289 VAL cc_start: 0.8969 (t) cc_final: 0.8652 (p) REVERT: C 473 TYR cc_start: 0.8171 (m-10) cc_final: 0.7668 (m-10) REVERT: C 495 TYR cc_start: 0.6866 (m-80) cc_final: 0.5821 (m-80) REVERT: C 497 PHE cc_start: 0.7613 (m-10) cc_final: 0.7382 (m-80) REVERT: C 869 MET cc_start: 0.9176 (mtt) cc_final: 0.8761 (mtt) REVERT: C 984 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8046 (mp) REVERT: E 3 GLN cc_start: 0.9123 (tp40) cc_final: 0.8639 (tp-100) REVERT: E 72 ASP cc_start: 0.7080 (t0) cc_final: 0.6638 (t0) REVERT: E 75 LYS cc_start: 0.9164 (mmmt) cc_final: 0.8867 (mmmt) REVERT: G 4 MET cc_start: 0.8104 (tpp) cc_final: 0.7769 (tpt) REVERT: G 21 ILE cc_start: 0.8817 (mp) cc_final: 0.8454 (tp) REVERT: G 35 TRP cc_start: 0.6670 (m100) cc_final: 0.6359 (m100) REVERT: G 42 GLN cc_start: 0.9206 (mt0) cc_final: 0.8859 (mp10) REVERT: G 54 ARG cc_start: 0.8591 (ttt90) cc_final: 0.8149 (tpp-160) REVERT: G 89 MET cc_start: 0.5432 (ttp) cc_final: 0.5136 (tmm) REVERT: G 93 HIS cc_start: 0.8821 (m90) cc_final: 0.8440 (m-70) outliers start: 84 outliers final: 63 residues processed: 424 average time/residue: 0.4426 time to fit residues: 302.3806 Evaluate side-chains 374 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 309 time to evaluate : 3.344 ------------------------------------------------------------------------------- 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 705 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR 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 983 ARG 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 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 54 ARG 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 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 595 VAL 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 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 984 LEU 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 75 ILE Chi-restraints excluded: chain C residue 127 VAL 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 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 959 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 1006 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 379 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 289 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 356 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 50 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 856 ASN C 901 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.101279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074482 restraints weight = 94226.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077318 restraints weight = 47220.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079216 restraints weight = 29903.900| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32754 Z= 0.134 Angle : 0.618 10.386 44676 Z= 0.311 Chirality : 0.044 0.367 5151 Planarity : 0.004 0.042 5682 Dihedral : 5.263 54.800 5628 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.50 % Rotamer: Outliers : 2.31 % Allowed : 11.26 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 3948 helix: 2.70 (0.20), residues: 654 sheet: 0.65 (0.16), residues: 927 loop : -0.53 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.004 0.001 HIS C1064 PHE 0.025 0.002 PHE B 497 TYR 0.029 0.001 TYR G 49 ARG 0.013 0.000 ARG C1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 45) link_NAG-ASN : angle 1.96339 ( 135) link_BETA1-4 : bond 0.00411 ( 18) link_BETA1-4 : angle 1.42018 ( 54) hydrogen bonds : bond 0.04211 ( 1317) hydrogen bonds : angle 5.46644 ( 3681) SS BOND : bond 0.00351 ( 54) SS BOND : angle 1.51504 ( 108) covalent geometry : bond 0.00307 (32637) covalent geometry : angle 0.60442 (44379) *********************** 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 425 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 345 time to evaluate : 3.558 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: A 138 ASP cc_start: 0.7742 (m-30) cc_final: 0.6918 (p0) REVERT: A 140 PHE cc_start: 0.7764 (p90) cc_final: 0.7073 (p90) REVERT: A 177 MET cc_start: 0.6290 (mmm) cc_final: 0.5300 (mmm) REVERT: A 223 LEU cc_start: 0.8205 (mt) cc_final: 0.7654 (tp) REVERT: A 269 TYR cc_start: 0.7040 (m-80) cc_final: 0.6782 (m-80) REVERT: A 289 VAL cc_start: 0.8814 (t) cc_final: 0.8409 (p) REVERT: A 402 ILE cc_start: 0.7592 (pt) cc_final: 0.7295 (pt) REVERT: A 473 TYR cc_start: 0.8307 (m-10) cc_final: 0.7697 (m-10) REVERT: A 495 TYR cc_start: 0.6340 (m-80) cc_final: 0.5499 (m-80) REVERT: A 762 GLN cc_start: 0.9097 (tt0) cc_final: 0.8553 (tm-30) REVERT: A 869 MET cc_start: 0.9107 (mtt) cc_final: 0.8856 (mtt) REVERT: A 968 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8517 (t) REVERT: H 34 MET cc_start: 0.6894 (ptp) cc_final: 0.6068 (pmm) REVERT: H 38 ARG cc_start: 0.8756 (ptt180) cc_final: 0.8345 (ptp90) REVERT: H 72 ASP cc_start: 0.7572 (t0) cc_final: 0.6524 (p0) REVERT: H 100 ASP cc_start: 0.8748 (t0) cc_final: 0.8470 (t0) REVERT: L 4 MET cc_start: 0.7926 (tpp) cc_final: 0.7528 (tpt) REVERT: L 35 TRP cc_start: 0.6439 (m100) cc_final: 0.6043 (m100) REVERT: L 42 GLN cc_start: 0.9099 (mt0) cc_final: 0.8746 (mp10) REVERT: L 74 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8443 (mttt) REVERT: L 89 MET cc_start: 0.5126 (ttp) cc_final: 0.4821 (tmm) REVERT: B 138 ASP cc_start: 0.7710 (m-30) cc_final: 0.7375 (p0) REVERT: B 177 MET cc_start: 0.6110 (mmt) cc_final: 0.5769 (mmt) REVERT: B 223 LEU cc_start: 0.8375 (mt) cc_final: 0.7733 (tp) REVERT: B 289 VAL cc_start: 0.8971 (t) cc_final: 0.8623 (p) REVERT: B 298 GLU cc_start: 0.7614 (pt0) cc_final: 0.7369 (pt0) REVERT: B 473 TYR cc_start: 0.7801 (m-10) cc_final: 0.7355 (m-10) REVERT: B 731 MET cc_start: 0.9055 (ptt) cc_final: 0.8773 (ptt) REVERT: B 869 MET cc_start: 0.9028 (mtt) cc_final: 0.8817 (mtt) REVERT: B 984 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 990 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7671 (tm-30) REVERT: D 38 ARG cc_start: 0.8500 (ptt180) cc_final: 0.8183 (ptt-90) REVERT: D 72 ASP cc_start: 0.7404 (t0) cc_final: 0.6212 (p0) REVERT: D 85 GLU cc_start: 0.7469 (pm20) cc_final: 0.6322 (pm20) REVERT: F 21 ILE cc_start: 0.9053 (mp) cc_final: 0.8612 (tp) REVERT: F 54 ARG cc_start: 0.8718 (ttt90) cc_final: 0.8104 (tpp-160) REVERT: F 61 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7720 (ttp-170) REVERT: F 83 VAL cc_start: 0.8854 (m) cc_final: 0.8562 (t) REVERT: F 93 HIS cc_start: 0.8654 (m90) cc_final: 0.8334 (m-70) REVERT: C 138 ASP cc_start: 0.7719 (m-30) cc_final: 0.7392 (p0) REVERT: C 140 PHE cc_start: 0.8005 (p90) cc_final: 0.7207 (p90) REVERT: C 177 MET cc_start: 0.5590 (mmt) cc_final: 0.5296 (mmt) REVERT: C 223 LEU cc_start: 0.8235 (mt) cc_final: 0.7942 (mp) REVERT: C 289 VAL cc_start: 0.8883 (t) cc_final: 0.8538 (p) REVERT: C 473 TYR cc_start: 0.8161 (m-10) cc_final: 0.7645 (m-10) REVERT: C 752 LEU cc_start: 0.8688 (mt) cc_final: 0.8264 (tp) REVERT: C 869 MET cc_start: 0.9190 (mtt) cc_final: 0.8803 (mtt) REVERT: C 984 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8072 (mp) REVERT: E 3 GLN cc_start: 0.9127 (tp40) cc_final: 0.8651 (tp-100) REVERT: E 34 MET cc_start: 0.6880 (ptp) cc_final: 0.6565 (ptp) REVERT: E 72 ASP cc_start: 0.7085 (t0) cc_final: 0.6631 (t0) REVERT: E 75 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8818 (mmmt) REVERT: G 4 MET cc_start: 0.8156 (tpp) cc_final: 0.7794 (tpt) REVERT: G 21 ILE cc_start: 0.8835 (mp) cc_final: 0.8493 (tp) REVERT: G 35 TRP cc_start: 0.6746 (m100) cc_final: 0.6270 (m100) REVERT: G 54 ARG cc_start: 0.8662 (ttt90) cc_final: 0.8221 (tpp-160) REVERT: G 74 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8323 (mttt) REVERT: G 93 HIS cc_start: 0.8832 (m90) cc_final: 0.8443 (m-70) outliers start: 80 outliers final: 57 residues processed: 402 average time/residue: 0.4618 time to fit residues: 295.4478 Evaluate side-chains 368 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 546 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 873 TYR 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 1006 THR 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 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 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 705 CYS 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 984 LEU 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 401 VAL 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 781 VAL 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 984 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 25 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 286 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 353 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 359 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1142 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B1142 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.096137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.070542 restraints weight = 98622.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.073058 restraints weight = 52140.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.074746 restraints weight = 34218.942| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 32754 Z= 0.269 Angle : 0.724 10.897 44676 Z= 0.369 Chirality : 0.046 0.300 5151 Planarity : 0.005 0.059 5682 Dihedral : 5.621 53.746 5628 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.00 % Favored : 95.92 % Rotamer: Outliers : 3.27 % Allowed : 10.85 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.13), residues: 3948 helix: 2.24 (0.20), residues: 654 sheet: 0.48 (0.16), residues: 918 loop : -0.70 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 103 HIS 0.011 0.002 HIS C1064 PHE 0.043 0.003 PHE A 497 TYR 0.034 0.002 TYR A 873 ARG 0.009 0.001 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00386 ( 45) link_NAG-ASN : angle 1.97506 ( 135) link_BETA1-4 : bond 0.00268 ( 18) link_BETA1-4 : angle 1.31852 ( 54) hydrogen bonds : bond 0.04893 ( 1317) hydrogen bonds : angle 5.73226 ( 3681) SS BOND : bond 0.00430 ( 54) SS BOND : angle 1.40291 ( 108) covalent geometry : bond 0.00614 (32637) covalent geometry : angle 0.71379 (44379) *********************** 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 437 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 324 time to evaluate : 3.264 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: A 223 LEU cc_start: 0.8378 (mt) cc_final: 0.7725 (tp) REVERT: A 269 TYR cc_start: 0.7110 (m-80) cc_final: 0.6772 (m-80) REVERT: A 289 VAL cc_start: 0.8941 (t) cc_final: 0.8552 (p) REVERT: A 318 PHE cc_start: 0.6771 (t80) cc_final: 0.6341 (t80) REVERT: A 473 TYR cc_start: 0.8397 (m-10) cc_final: 0.7803 (m-10) REVERT: A 486 PHE cc_start: 0.7837 (t80) cc_final: 0.7620 (t80) REVERT: A 501 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.7890 (p0) REVERT: A 762 GLN cc_start: 0.9116 (tt0) cc_final: 0.8658 (tm-30) REVERT: H 34 MET cc_start: 0.7117 (ptp) cc_final: 0.6849 (ptp) REVERT: H 72 ASP cc_start: 0.7481 (t0) cc_final: 0.6369 (p0) REVERT: H 77 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7530 (m) REVERT: H 100 ASP cc_start: 0.8662 (t0) cc_final: 0.8255 (t0) REVERT: L 4 MET cc_start: 0.7778 (tpp) cc_final: 0.7284 (tpt) REVERT: L 35 TRP cc_start: 0.6720 (m100) cc_final: 0.6350 (m100) REVERT: L 42 GLN cc_start: 0.9127 (mt0) cc_final: 0.8782 (mp10) REVERT: L 50 GLN cc_start: 0.9467 (mp10) cc_final: 0.8740 (mp10) REVERT: L 89 MET cc_start: 0.5158 (ttp) cc_final: 0.4834 (tmm) REVERT: B 138 ASP cc_start: 0.7909 (m-30) cc_final: 0.7565 (p0) REVERT: B 177 MET cc_start: 0.6249 (mmt) cc_final: 0.5762 (mmt) REVERT: B 223 LEU cc_start: 0.8466 (mt) cc_final: 0.7840 (tp) REVERT: B 289 VAL cc_start: 0.8985 (t) cc_final: 0.8669 (p) REVERT: B 298 GLU cc_start: 0.7952 (pt0) cc_final: 0.7708 (pt0) REVERT: B 473 TYR cc_start: 0.7969 (m-10) cc_final: 0.7624 (m-10) REVERT: B 486 PHE cc_start: 0.7615 (t80) cc_final: 0.7274 (t80) REVERT: B 869 MET cc_start: 0.9017 (mtt) cc_final: 0.8726 (mtt) REVERT: B 990 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7724 (tm-30) REVERT: D 64 GLU cc_start: 0.8724 (tt0) cc_final: 0.8467 (tp30) REVERT: D 72 ASP cc_start: 0.7386 (t0) cc_final: 0.6217 (p0) REVERT: F 35 TRP cc_start: 0.6807 (m100) cc_final: 0.6526 (m100) REVERT: F 54 ARG cc_start: 0.8704 (ttt90) cc_final: 0.8192 (tpp-160) REVERT: F 83 VAL cc_start: 0.8841 (m) cc_final: 0.8545 (t) REVERT: F 93 HIS cc_start: 0.8931 (m90) cc_final: 0.8561 (m-70) REVERT: C 138 ASP cc_start: 0.7825 (m-30) cc_final: 0.7278 (p0) REVERT: C 140 PHE cc_start: 0.8057 (p90) cc_final: 0.7124 (p90) REVERT: C 177 MET cc_start: 0.5825 (mmt) cc_final: 0.5445 (mmt) REVERT: C 223 LEU cc_start: 0.8322 (mt) cc_final: 0.7893 (tp) REVERT: C 289 VAL cc_start: 0.8969 (t) cc_final: 0.8663 (p) REVERT: C 473 TYR cc_start: 0.8261 (m-10) cc_final: 0.7766 (m-10) REVERT: C 486 PHE cc_start: 0.7991 (t80) cc_final: 0.7633 (t80) REVERT: C 869 MET cc_start: 0.9124 (mtt) cc_final: 0.8851 (mtt) REVERT: C 984 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8172 (mp) REVERT: E 3 GLN cc_start: 0.9167 (tp40) cc_final: 0.8843 (tp-100) REVERT: E 64 GLU cc_start: 0.8795 (tt0) cc_final: 0.8538 (tp30) REVERT: E 72 ASP cc_start: 0.7084 (t0) cc_final: 0.6622 (t0) REVERT: E 75 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8829 (mmmt) REVERT: E 85 GLU cc_start: 0.6805 (pm20) cc_final: 0.6320 (pm20) REVERT: G 4 MET cc_start: 0.8192 (tpp) cc_final: 0.7880 (tpt) REVERT: G 35 TRP cc_start: 0.6852 (m100) cc_final: 0.6462 (m100) REVERT: G 61 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7867 (ttp-170) REVERT: G 89 MET cc_start: 0.5680 (ttp) cc_final: 0.5398 (tmm) REVERT: G 93 HIS cc_start: 0.8881 (m90) cc_final: 0.8533 (m-70) outliers start: 113 outliers final: 76 residues processed: 403 average time/residue: 0.4392 time to fit residues: 283.2227 Evaluate side-chains 382 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 302 time to evaluate : 3.270 ------------------------------------------------------------------------------- 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 312 ILE 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 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 873 TYR 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 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 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 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 738 CYS Chi-restraints excluded: chain B residue 781 VAL 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 B residue 1141 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 1 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 202 LYS 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 461 LEU 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 595 VAL Chi-restraints excluded: chain C residue 597 VAL 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 959 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 1006 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 75 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 330 optimal weight: 0.7980 chunk 107 optimal weight: 0.4980 chunk 345 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 389 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 311 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 A1054 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 960 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.099376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.073941 restraints weight = 94403.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076544 restraints weight = 49477.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.078285 restraints weight = 32189.310| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32754 Z= 0.123 Angle : 0.615 10.828 44676 Z= 0.310 Chirality : 0.045 0.233 5151 Planarity : 0.004 0.050 5682 Dihedral : 5.433 55.074 5628 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 2.00 % Allowed : 12.44 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 3948 helix: 2.53 (0.20), residues: 672 sheet: 0.58 (0.16), residues: 921 loop : -0.77 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 64 HIS 0.007 0.001 HIS C 519 PHE 0.048 0.002 PHE C 497 TYR 0.030 0.001 TYR L 49 ARG 0.007 0.000 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 45) link_NAG-ASN : angle 1.71772 ( 135) link_BETA1-4 : bond 0.00439 ( 18) link_BETA1-4 : angle 1.23588 ( 54) hydrogen bonds : bond 0.04261 ( 1317) hydrogen bonds : angle 5.41251 ( 3681) SS BOND : bond 0.00257 ( 54) SS BOND : angle 1.30054 ( 108) covalent geometry : bond 0.00276 (32637) covalent geometry : angle 0.60531 (44379) *********************** 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 417 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 348 time to evaluate : 3.595 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: A 138 ASP cc_start: 0.7831 (m-30) cc_final: 0.7166 (p0) REVERT: A 177 MET cc_start: 0.6202 (mmt) cc_final: 0.5568 (mmt) REVERT: A 216 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6306 (tt) REVERT: A 223 LEU cc_start: 0.8323 (mt) cc_final: 0.7811 (tp) REVERT: A 269 TYR cc_start: 0.7183 (m-80) cc_final: 0.6888 (m-80) REVERT: A 289 VAL cc_start: 0.8798 (t) cc_final: 0.8414 (p) REVERT: A 473 TYR cc_start: 0.8317 (m-10) cc_final: 0.7704 (m-10) REVERT: A 486 PHE cc_start: 0.7758 (t80) cc_final: 0.7543 (t80) REVERT: A 501 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7885 (p0) REVERT: A 1011 GLN cc_start: 0.8852 (tp40) cc_final: 0.8352 (tp40) REVERT: H 34 MET cc_start: 0.7245 (ptp) cc_final: 0.6998 (ptp) REVERT: H 72 ASP cc_start: 0.7568 (t0) cc_final: 0.6457 (p0) REVERT: H 77 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7525 (m) REVERT: H 100 ASP cc_start: 0.8591 (t0) cc_final: 0.8320 (t0) REVERT: L 4 MET cc_start: 0.7757 (tpp) cc_final: 0.7304 (tpt) REVERT: L 35 TRP cc_start: 0.6464 (m100) cc_final: 0.6154 (m100) REVERT: L 50 GLN cc_start: 0.9434 (mp10) cc_final: 0.9210 (mp10) REVERT: L 53 ASN cc_start: 0.9129 (t0) cc_final: 0.8882 (t0) REVERT: L 89 MET cc_start: 0.5376 (ttp) cc_final: 0.4948 (tmm) REVERT: B 138 ASP cc_start: 0.7826 (m-30) cc_final: 0.7535 (p0) REVERT: B 177 MET cc_start: 0.6052 (mmt) cc_final: 0.5627 (mmt) REVERT: B 223 LEU cc_start: 0.8374 (mt) cc_final: 0.7749 (tp) REVERT: B 289 VAL cc_start: 0.8866 (t) cc_final: 0.8569 (p) REVERT: B 473 TYR cc_start: 0.8042 (m-10) cc_final: 0.7501 (m-10) REVERT: B 486 PHE cc_start: 0.7600 (t80) cc_final: 0.7254 (t80) REVERT: B 731 MET cc_start: 0.9204 (ptt) cc_final: 0.8938 (ptt) REVERT: B 867 ASP cc_start: 0.8294 (m-30) cc_final: 0.8002 (p0) REVERT: B 990 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7673 (tm-30) REVERT: D 67 PHE cc_start: 0.4068 (OUTLIER) cc_final: 0.3490 (m-80) REVERT: D 72 ASP cc_start: 0.7379 (t0) cc_final: 0.6275 (p0) REVERT: F 21 ILE cc_start: 0.9079 (mp) cc_final: 0.8689 (tp) REVERT: F 35 TRP cc_start: 0.6753 (m100) cc_final: 0.6434 (m100) REVERT: F 54 ARG cc_start: 0.8740 (ttt90) cc_final: 0.8231 (tpt170) REVERT: F 83 VAL cc_start: 0.8688 (m) cc_final: 0.8400 (t) REVERT: F 93 HIS cc_start: 0.8867 (m90) cc_final: 0.8524 (m-70) REVERT: C 138 ASP cc_start: 0.7724 (m-30) cc_final: 0.7341 (p0) REVERT: C 140 PHE cc_start: 0.7993 (p90) cc_final: 0.7084 (p90) REVERT: C 177 MET cc_start: 0.5680 (mmt) cc_final: 0.5328 (mmt) REVERT: C 223 LEU cc_start: 0.8364 (mt) cc_final: 0.7966 (tp) REVERT: C 289 VAL cc_start: 0.8839 (t) cc_final: 0.8516 (p) REVERT: C 473 TYR cc_start: 0.8253 (m-10) cc_final: 0.7685 (m-10) REVERT: C 486 PHE cc_start: 0.7962 (t80) cc_final: 0.7607 (t80) REVERT: C 869 MET cc_start: 0.9188 (mtt) cc_final: 0.8789 (mtt) REVERT: C 984 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8070 (mp) REVERT: E 3 GLN cc_start: 0.9173 (tp40) cc_final: 0.8825 (tp-100) REVERT: E 72 ASP cc_start: 0.7081 (t0) cc_final: 0.6651 (t0) REVERT: E 75 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8924 (mmmt) REVERT: G 4 MET cc_start: 0.8186 (tpp) cc_final: 0.7860 (tpt) REVERT: G 35 TRP cc_start: 0.6821 (m100) cc_final: 0.6387 (m100) REVERT: G 74 LYS cc_start: 0.8613 (mmtt) cc_final: 0.8349 (mttt) REVERT: G 93 HIS cc_start: 0.8838 (m90) cc_final: 0.8494 (m-70) outliers start: 69 outliers final: 50 residues processed: 393 average time/residue: 0.4719 time to fit residues: 297.9949 Evaluate side-chains 368 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 3.461 ------------------------------------------------------------------------------- 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 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 873 TYR 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 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 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 738 CYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 501 ASN 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 959 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 E residue 11 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 Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 209 optimal weight: 7.9990 chunk 116 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 252 optimal weight: 0.6980 chunk 298 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 357 optimal weight: 0.0980 chunk 65 optimal weight: 6.9990 chunk 335 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** B 196 ASN B 501 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN C 856 ASN ** 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 = 0.3814 r_free = 0.3814 target = 0.097305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071676 restraints weight = 94965.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.074197 restraints weight = 50382.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075914 restraints weight = 32996.104| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 32754 Z= 0.175 Angle : 0.645 15.826 44676 Z= 0.325 Chirality : 0.045 0.348 5151 Planarity : 0.004 0.041 5682 Dihedral : 5.463 54.971 5628 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 2.00 % Allowed : 12.96 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 3948 helix: 2.48 (0.20), residues: 672 sheet: 0.54 (0.16), residues: 933 loop : -0.81 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 103 HIS 0.006 0.001 HIS C1064 PHE 0.064 0.002 PHE B 497 TYR 0.043 0.002 TYR F 49 ARG 0.008 0.001 ARG C 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 45) link_NAG-ASN : angle 1.73461 ( 135) link_BETA1-4 : bond 0.00369 ( 18) link_BETA1-4 : angle 1.19993 ( 54) hydrogen bonds : bond 0.04323 ( 1317) hydrogen bonds : angle 5.42147 ( 3681) SS BOND : bond 0.00477 ( 54) SS BOND : angle 1.50262 ( 108) covalent geometry : bond 0.00406 (32637) covalent geometry : angle 0.63437 (44379) *********************** 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 391 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 322 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7992 (m-30) cc_final: 0.7246 (p0) REVERT: A 177 MET cc_start: 0.6369 (mmt) cc_final: 0.5729 (mmt) REVERT: A 216 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6415 (tt) REVERT: A 223 LEU cc_start: 0.8416 (mt) cc_final: 0.7949 (tp) REVERT: A 269 TYR cc_start: 0.7167 (m-80) cc_final: 0.6820 (m-80) REVERT: A 289 VAL cc_start: 0.8850 (t) cc_final: 0.8474 (p) REVERT: A 473 TYR cc_start: 0.8367 (m-10) cc_final: 0.7757 (m-10) REVERT: A 486 PHE cc_start: 0.7746 (t80) cc_final: 0.7515 (t80) REVERT: A 869 MET cc_start: 0.9066 (mtm) cc_final: 0.8774 (mtt) REVERT: H 34 MET cc_start: 0.7275 (ptp) cc_final: 0.7014 (ptp) REVERT: H 72 ASP cc_start: 0.7464 (t0) cc_final: 0.6280 (p0) REVERT: H 100 ASP cc_start: 0.8574 (t0) cc_final: 0.8315 (t0) REVERT: L 3 VAL cc_start: 0.9318 (t) cc_final: 0.9095 (p) REVERT: L 4 MET cc_start: 0.7656 (tpp) cc_final: 0.7293 (tpt) REVERT: L 21 ILE cc_start: 0.8640 (mp) cc_final: 0.8328 (tp) REVERT: L 35 TRP cc_start: 0.6592 (m100) cc_final: 0.6052 (m100) REVERT: L 50 GLN cc_start: 0.9462 (mp10) cc_final: 0.9183 (mp10) REVERT: L 53 ASN cc_start: 0.9167 (t0) cc_final: 0.8801 (t0) REVERT: L 89 MET cc_start: 0.5524 (ttp) cc_final: 0.5146 (tmm) REVERT: B 138 ASP cc_start: 0.7867 (m-30) cc_final: 0.7549 (p0) REVERT: B 177 MET cc_start: 0.6065 (mmt) cc_final: 0.5628 (mmt) REVERT: B 223 LEU cc_start: 0.8409 (mt) cc_final: 0.7779 (tp) REVERT: B 289 VAL cc_start: 0.8896 (t) cc_final: 0.8593 (p) REVERT: B 473 TYR cc_start: 0.8086 (m-10) cc_final: 0.7509 (m-10) REVERT: B 486 PHE cc_start: 0.7640 (t80) cc_final: 0.7269 (t80) REVERT: B 867 ASP cc_start: 0.8293 (m-30) cc_final: 0.8063 (p0) REVERT: B 990 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7719 (tm-30) REVERT: D 64 GLU cc_start: 0.8629 (tt0) cc_final: 0.8351 (tp30) REVERT: D 67 PHE cc_start: 0.3975 (OUTLIER) cc_final: 0.3619 (m-80) REVERT: D 72 ASP cc_start: 0.7386 (t0) cc_final: 0.6292 (p0) REVERT: D 77 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7723 (m) REVERT: F 21 ILE cc_start: 0.8881 (mp) cc_final: 0.8496 (tp) REVERT: F 35 TRP cc_start: 0.6760 (m100) cc_final: 0.6424 (m100) REVERT: F 54 ARG cc_start: 0.8403 (ttt90) cc_final: 0.7798 (tpt-90) REVERT: F 61 ARG cc_start: 0.8467 (ptp-170) cc_final: 0.7942 (ttp-170) REVERT: F 83 VAL cc_start: 0.8495 (m) cc_final: 0.8153 (t) REVERT: F 89 MET cc_start: 0.5135 (tmm) cc_final: 0.4676 (tmm) REVERT: F 93 HIS cc_start: 0.8889 (m90) cc_final: 0.8562 (m-70) REVERT: C 138 ASP cc_start: 0.7768 (m-30) cc_final: 0.7373 (p0) REVERT: C 140 PHE cc_start: 0.7971 (p90) cc_final: 0.7161 (p90) REVERT: C 177 MET cc_start: 0.5603 (mmt) cc_final: 0.5269 (mmt) REVERT: C 216 LEU cc_start: 0.6936 (mp) cc_final: 0.6639 (tt) REVERT: C 223 LEU cc_start: 0.8348 (mt) cc_final: 0.7933 (tp) REVERT: C 289 VAL cc_start: 0.8912 (t) cc_final: 0.8566 (p) REVERT: C 473 TYR cc_start: 0.8253 (m-10) cc_final: 0.7678 (m-10) REVERT: C 486 PHE cc_start: 0.7912 (t80) cc_final: 0.7558 (t80) REVERT: C 571 ASP cc_start: 0.8393 (m-30) cc_final: 0.7941 (t0) REVERT: C 869 MET cc_start: 0.9188 (mtt) cc_final: 0.8985 (mtt) REVERT: C 984 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8073 (mp) REVERT: E 3 GLN cc_start: 0.9203 (tp40) cc_final: 0.8857 (tp-100) REVERT: E 72 ASP cc_start: 0.7131 (t0) cc_final: 0.6688 (t0) REVERT: E 75 LYS cc_start: 0.9138 (mmmt) cc_final: 0.8902 (mmmt) REVERT: G 4 MET cc_start: 0.8203 (tpp) cc_final: 0.7852 (tpt) REVERT: G 61 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7855 (ttp80) REVERT: G 74 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8348 (mttt) REVERT: G 77 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8156 (tmt170) REVERT: G 93 HIS cc_start: 0.8817 (m90) cc_final: 0.8512 (m-70) REVERT: G 104 LEU cc_start: 0.8944 (tt) cc_final: 0.8628 (tt) outliers start: 69 outliers final: 55 residues processed: 369 average time/residue: 0.4472 time to fit residues: 263.7369 Evaluate side-chains 367 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 3.563 ------------------------------------------------------------------------------- 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 434 ILE Chi-restraints excluded: chain A residue 445 VAL 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 873 TYR 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 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 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 501 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 781 VAL 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 D residue 67 PHE Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 267 VAL 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 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 968 SER Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 340 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 299 optimal weight: 3.9990 chunk 259 optimal weight: 6.9990 chunk 393 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 334 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 501 ASN B1010 GLN ** 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 = 0.3801 r_free = 0.3801 target = 0.096570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.070944 restraints weight = 95593.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073449 restraints weight = 50844.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.075145 restraints weight = 33331.858| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 32754 Z= 0.186 Angle : 0.654 17.082 44676 Z= 0.330 Chirality : 0.046 0.328 5151 Planarity : 0.004 0.081 5682 Dihedral : 5.555 54.356 5628 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.23 % Favored : 95.67 % Rotamer: Outliers : 2.03 % Allowed : 13.25 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 3948 helix: 2.38 (0.20), residues: 672 sheet: 0.46 (0.16), residues: 930 loop : -0.85 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 103 HIS 0.007 0.001 HIS C1064 PHE 0.058 0.002 PHE B 497 TYR 0.035 0.002 TYR G 49 ARG 0.007 0.001 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 45) link_NAG-ASN : angle 1.71345 ( 135) link_BETA1-4 : bond 0.00311 ( 18) link_BETA1-4 : angle 1.15009 ( 54) hydrogen bonds : bond 0.04391 ( 1317) hydrogen bonds : angle 5.45547 ( 3681) SS BOND : bond 0.00415 ( 54) SS BOND : angle 1.43878 ( 108) covalent geometry : bond 0.00428 (32637) covalent geometry : angle 0.64439 (44379) *********************** 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 386 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 3.284 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: A 138 ASP cc_start: 0.8129 (m-30) cc_final: 0.7311 (p0) REVERT: A 140 PHE cc_start: 0.7715 (p90) cc_final: 0.7150 (p90) REVERT: A 177 MET cc_start: 0.6279 (mmt) cc_final: 0.5676 (mmt) REVERT: A 216 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6411 (tt) REVERT: A 223 LEU cc_start: 0.8427 (mt) cc_final: 0.7969 (tp) REVERT: A 269 TYR cc_start: 0.7228 (m-80) cc_final: 0.6901 (m-80) REVERT: A 289 VAL cc_start: 0.8870 (t) cc_final: 0.8485 (p) REVERT: A 473 TYR cc_start: 0.8375 (m-10) cc_final: 0.7807 (m-10) REVERT: A 486 PHE cc_start: 0.7894 (t80) cc_final: 0.7620 (t80) REVERT: A 869 MET cc_start: 0.9011 (mtm) cc_final: 0.8731 (mtt) REVERT: H 34 MET cc_start: 0.7332 (ptp) cc_final: 0.7076 (ptp) REVERT: H 72 ASP cc_start: 0.7446 (t0) cc_final: 0.6203 (p0) REVERT: L 4 MET cc_start: 0.7651 (tpp) cc_final: 0.7292 (tpt) REVERT: L 21 ILE cc_start: 0.8503 (mp) cc_final: 0.8294 (tp) REVERT: L 35 TRP cc_start: 0.6673 (m100) cc_final: 0.6181 (m100) REVERT: L 50 GLN cc_start: 0.9477 (mp10) cc_final: 0.9206 (mp10) REVERT: L 53 ASN cc_start: 0.9138 (t0) cc_final: 0.8767 (t0) REVERT: L 61 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7715 (ttp80) REVERT: L 89 MET cc_start: 0.5422 (ttp) cc_final: 0.5110 (tmm) REVERT: B 138 ASP cc_start: 0.7919 (m-30) cc_final: 0.7545 (p0) REVERT: B 177 MET cc_start: 0.6138 (mmt) cc_final: 0.5696 (mmt) REVERT: B 223 LEU cc_start: 0.8453 (mt) cc_final: 0.7895 (tp) REVERT: B 289 VAL cc_start: 0.8897 (t) cc_final: 0.8599 (p) REVERT: B 473 TYR cc_start: 0.8133 (m-10) cc_final: 0.7549 (m-10) REVERT: B 486 PHE cc_start: 0.7769 (t80) cc_final: 0.7408 (t80) REVERT: B 731 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8955 (ptt) REVERT: B 867 ASP cc_start: 0.8328 (m-30) cc_final: 0.8124 (p0) REVERT: B 990 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7720 (tm-30) REVERT: D 34 MET cc_start: 0.7147 (ptp) cc_final: 0.6703 (pmm) REVERT: D 64 GLU cc_start: 0.8697 (tt0) cc_final: 0.8431 (tp30) REVERT: D 72 ASP cc_start: 0.7379 (t0) cc_final: 0.6275 (p0) REVERT: D 77 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7727 (m) REVERT: F 21 ILE cc_start: 0.8920 (mp) cc_final: 0.8519 (tp) REVERT: F 35 TRP cc_start: 0.6862 (m100) cc_final: 0.6395 (m100) REVERT: F 54 ARG cc_start: 0.8501 (ttt90) cc_final: 0.8283 (ttt-90) REVERT: F 83 VAL cc_start: 0.8483 (m) cc_final: 0.8141 (t) REVERT: F 89 MET cc_start: 0.5332 (tmm) cc_final: 0.4900 (tmm) REVERT: F 93 HIS cc_start: 0.8841 (m90) cc_final: 0.8548 (m-70) REVERT: C 138 ASP cc_start: 0.7821 (m-30) cc_final: 0.7403 (p0) REVERT: C 140 PHE cc_start: 0.7972 (p90) cc_final: 0.7176 (p90) REVERT: C 177 MET cc_start: 0.5653 (mmt) cc_final: 0.5303 (mmt) REVERT: C 216 LEU cc_start: 0.6893 (mp) cc_final: 0.6652 (tt) REVERT: C 223 LEU cc_start: 0.8383 (mt) cc_final: 0.7954 (tp) REVERT: C 289 VAL cc_start: 0.8929 (t) cc_final: 0.8593 (p) REVERT: C 473 TYR cc_start: 0.8270 (m-10) cc_final: 0.7698 (m-10) REVERT: C 486 PHE cc_start: 0.7970 (t80) cc_final: 0.7650 (t80) REVERT: C 571 ASP cc_start: 0.8383 (m-30) cc_final: 0.7916 (t0) REVERT: C 869 MET cc_start: 0.9138 (mtt) cc_final: 0.8938 (mtt) REVERT: C 984 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8113 (mp) REVERT: E 72 ASP cc_start: 0.7166 (t0) cc_final: 0.6730 (t0) REVERT: E 75 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8862 (mmmt) REVERT: G 4 MET cc_start: 0.8276 (tpp) cc_final: 0.7929 (tpt) REVERT: G 35 TRP cc_start: 0.6780 (m100) cc_final: 0.6416 (m100) REVERT: G 61 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8011 (ttp80) REVERT: G 74 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8383 (mttt) REVERT: G 93 HIS cc_start: 0.8838 (m90) cc_final: 0.8520 (m-70) outliers start: 70 outliers final: 57 residues processed: 364 average time/residue: 0.4887 time to fit residues: 283.8640 Evaluate side-chains 358 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 296 time to evaluate : 3.253 ------------------------------------------------------------------------------- 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 434 ILE Chi-restraints excluded: chain A residue 445 VAL 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 873 TYR 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 H residue 61 ASP Chi-restraints excluded: chain H residue 67 PHE Chi-restraints excluded: chain L residue 27 LEU 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 501 ASN Chi-restraints excluded: chain B residue 524 VAL 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 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 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 75 ILE Chi-restraints excluded: chain C residue 202 LYS 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 524 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 959 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 E residue 67 PHE Chi-restraints excluded: chain E residue 95 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 172 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 216 optimal weight: 0.6980 chunk 383 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 311 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 242 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN H 81 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** 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 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3838 r_free = 0.3838 target = 0.098605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.072968 restraints weight = 94715.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075525 restraints weight = 50605.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077238 restraints weight = 33319.222| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32754 Z= 0.122 Angle : 0.633 18.008 44676 Z= 0.317 Chirality : 0.045 0.310 5151 Planarity : 0.004 0.052 5682 Dihedral : 5.478 55.187 5628 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 1.56 % Allowed : 13.89 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 3948 helix: 2.63 (0.21), residues: 654 sheet: 0.55 (0.16), residues: 927 loop : -0.77 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.004 0.001 HIS C 519 PHE 0.043 0.002 PHE B 497 TYR 0.032 0.002 TYR G 49 ARG 0.014 0.000 ARG L 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 45) link_NAG-ASN : angle 1.64129 ( 135) link_BETA1-4 : bond 0.00408 ( 18) link_BETA1-4 : angle 1.13738 ( 54) hydrogen bonds : bond 0.04116 ( 1317) hydrogen bonds : angle 5.29757 ( 3681) SS BOND : bond 0.00349 ( 54) SS BOND : angle 1.31036 ( 108) covalent geometry : bond 0.00276 (32637) covalent geometry : angle 0.62363 (44379) ********************** 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 390 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 336 time to evaluate : 3.747 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 138 ASP cc_start: 0.8079 (m-30) cc_final: 0.7288 (p0) REVERT: A 140 PHE cc_start: 0.7777 (p90) cc_final: 0.7247 (p90) REVERT: A 177 MET cc_start: 0.6030 (mmt) cc_final: 0.5313 (mmt) REVERT: A 216 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6469 (tt) REVERT: A 223 LEU cc_start: 0.8382 (mt) cc_final: 0.8030 (mt) REVERT: A 269 TYR cc_start: 0.7266 (m-80) cc_final: 0.6894 (m-80) REVERT: A 289 VAL cc_start: 0.8757 (t) cc_final: 0.8376 (p) REVERT: A 473 TYR cc_start: 0.8322 (m-10) cc_final: 0.7748 (m-10) REVERT: A 486 PHE cc_start: 0.7712 (t80) cc_final: 0.7465 (t80) REVERT: H 34 MET cc_start: 0.7349 (ptp) cc_final: 0.7097 (ptp) REVERT: H 38 ARG cc_start: 0.8911 (ptt180) cc_final: 0.8416 (ptp90) REVERT: H 72 ASP cc_start: 0.7479 (t0) cc_final: 0.6206 (p0) REVERT: L 4 MET cc_start: 0.7641 (tpp) cc_final: 0.7367 (tpt) REVERT: L 21 ILE cc_start: 0.8677 (mp) cc_final: 0.8262 (tp) REVERT: L 35 TRP cc_start: 0.6553 (m100) cc_final: 0.6073 (m100) REVERT: L 50 GLN cc_start: 0.9449 (mp10) cc_final: 0.9171 (mp10) REVERT: L 53 ASN cc_start: 0.9164 (t0) cc_final: 0.8762 (t0) REVERT: L 61 ARG cc_start: 0.8124 (ttp-110) cc_final: 0.7762 (ttp80) REVERT: B 138 ASP cc_start: 0.7868 (m-30) cc_final: 0.7536 (p0) REVERT: B 177 MET cc_start: 0.6048 (mmt) cc_final: 0.5610 (mmt) REVERT: B 223 LEU cc_start: 0.8366 (mt) cc_final: 0.7825 (tp) REVERT: B 289 VAL cc_start: 0.8839 (t) cc_final: 0.8532 (p) REVERT: B 473 TYR cc_start: 0.8105 (m-10) cc_final: 0.7538 (m-10) REVERT: B 486 PHE cc_start: 0.7725 (t80) cc_final: 0.7368 (t80) REVERT: B 731 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8942 (ptt) REVERT: B 990 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7885 (tm-30) REVERT: D 34 MET cc_start: 0.7104 (ptp) cc_final: 0.6745 (pmm) REVERT: D 64 GLU cc_start: 0.8647 (tt0) cc_final: 0.8381 (tp30) REVERT: D 72 ASP cc_start: 0.7393 (t0) cc_final: 0.6304 (p0) REVERT: D 77 THR cc_start: 0.8129 (OUTLIER) cc_final: 0.7723 (m) REVERT: F 21 ILE cc_start: 0.8921 (mp) cc_final: 0.8538 (tp) REVERT: F 35 TRP cc_start: 0.6832 (m100) cc_final: 0.6405 (m100) REVERT: F 89 MET cc_start: 0.5457 (tmm) cc_final: 0.5098 (tmm) REVERT: F 93 HIS cc_start: 0.8803 (m90) cc_final: 0.8498 (m-70) REVERT: C 138 ASP cc_start: 0.7757 (m-30) cc_final: 0.7379 (p0) REVERT: C 140 PHE cc_start: 0.7917 (p90) cc_final: 0.7144 (p90) REVERT: C 177 MET cc_start: 0.5631 (mmt) cc_final: 0.5302 (mmt) REVERT: C 216 LEU cc_start: 0.6901 (mp) cc_final: 0.6622 (tt) REVERT: C 223 LEU cc_start: 0.8427 (mt) cc_final: 0.8058 (tp) REVERT: C 289 VAL cc_start: 0.8897 (t) cc_final: 0.8533 (p) REVERT: C 473 TYR cc_start: 0.8225 (m-10) cc_final: 0.7651 (m-10) REVERT: C 486 PHE cc_start: 0.7927 (t80) cc_final: 0.7612 (t80) REVERT: C 571 ASP cc_start: 0.8370 (m-30) cc_final: 0.7882 (t0) REVERT: C 984 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8094 (mp) REVERT: E 3 GLN cc_start: 0.9230 (tp40) cc_final: 0.8875 (tp-100) REVERT: E 34 MET cc_start: 0.6968 (ptp) cc_final: 0.6307 (pmm) REVERT: E 72 ASP cc_start: 0.7139 (t0) cc_final: 0.6711 (t0) REVERT: E 75 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8815 (mmmt) REVERT: G 4 MET cc_start: 0.8256 (tpp) cc_final: 0.7898 (tpt) REVERT: G 35 TRP cc_start: 0.6685 (m100) cc_final: 0.6345 (m100) REVERT: G 61 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8023 (ttp80) REVERT: G 74 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8403 (mttt) REVERT: G 83 VAL cc_start: 0.8885 (m) cc_final: 0.8541 (t) REVERT: G 93 HIS cc_start: 0.8819 (m90) cc_final: 0.8506 (m-70) outliers start: 54 outliers final: 48 residues processed: 372 average time/residue: 0.4539 time to fit residues: 270.2676 Evaluate side-chains 367 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 3.467 ------------------------------------------------------------------------------- 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 445 VAL 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 873 TYR 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 H residue 61 ASP Chi-restraints excluded: chain H residue 67 PHE 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 501 ASN Chi-restraints excluded: chain B residue 524 VAL 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 959 LEU Chi-restraints excluded: chain B residue 968 SER 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 95 ASP Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 597 VAL 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 973 ILE Chi-restraints excluded: chain C residue 984 LEU 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 E residue 109 VAL Chi-restraints excluded: chain G residue 61 ARG Chi-restraints excluded: chain G residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 229 optimal weight: 2.9990 chunk 328 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 340 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 347 optimal weight: 0.0170 chunk 330 optimal weight: 0.3980 chunk 311 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.100900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.073732 restraints weight = 100608.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.076432 restraints weight = 53187.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.078245 restraints weight = 34896.689| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32754 Z= 0.154 Angle : 0.646 17.078 44676 Z= 0.323 Chirality : 0.045 0.302 5151 Planarity : 0.004 0.056 5682 Dihedral : 5.488 54.720 5628 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.93 % Favored : 96.00 % Rotamer: Outliers : 1.65 % Allowed : 14.35 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 3948 helix: 2.53 (0.21), residues: 654 sheet: 0.55 (0.16), residues: 924 loop : -0.79 (0.12), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 103 HIS 0.006 0.001 HIS A1064 PHE 0.045 0.002 PHE B 497 TYR 0.047 0.002 TYR C 904 ARG 0.007 0.001 ARG E 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 45) link_NAG-ASN : angle 1.64793 ( 135) link_BETA1-4 : bond 0.00351 ( 18) link_BETA1-4 : angle 1.12948 ( 54) hydrogen bonds : bond 0.04174 ( 1317) hydrogen bonds : angle 5.30298 ( 3681) SS BOND : bond 0.00350 ( 54) SS BOND : angle 1.31396 ( 108) covalent geometry : bond 0.00356 (32637) covalent geometry : angle 0.63724 (44379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11262.97 seconds wall clock time: 197 minutes 13.70 seconds (11833.70 seconds total)