Starting phenix.real_space_refine on Sun Jul 5 00:13:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.cif Found real_map, /net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.map" model { file = "/net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7usa_26730/07_2026/7usa_26730.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.085 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 126 5.16 5 C 15453 2.51 5 N 3973 2.21 5 O 4755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 165 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24307 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 7694 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 40, 'TRANS': 1020} Chain breaks: 10 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 395 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASN:plan1': 18, 'GLU:plan': 18, 'PHE:plan': 3, 'ARG:plan': 7, 'ASP:plan': 31, 'GLN:plan1': 8, 'TYR:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 343 Chain: "B" Number of atoms: 7678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 7678 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 40, 'TRANS': 1017} Chain breaks: 10 Unresolved non-hydrogen bonds: 495 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ASN:plan1': 12, 'GLU:plan': 19, 'TYR:plan': 3, 'ARG:plan': 8, 'ASP:plan': 29, 'GLN:plan1': 9, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 317 Chain: "C" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7693 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 40, 'TRANS': 1021} Chain breaks: 10 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ASN:plan1': 16, 'GLU:plan': 19, 'TYR:plan': 4, 'ARG:plan': 7, 'ASP:plan': 27, 'GLN:plan1': 11, 'PHE:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 333 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 5.66, per 1000 atoms: 0.23 Number of scatterers: 24307 At special positions: 0 Unit cell: (144.996, 153.426, 157.641, 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 126 16.00 O 4755 8.00 N 3973 7.00 C 15453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.13 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 444 " distance=2.11 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 626 " distance=2.05 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 594 " distance=2.07 Simple disulfide: pdb=" SG CYS A 609 " - pdb=" SG CYS A 636 " distance=2.04 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 809 " distance=2.03 Simple disulfide: pdb=" SG CYS A 860 " - pdb=" SG CYS A 882 " distance=2.16 Simple disulfide: pdb=" SG CYS A 865 " - pdb=" SG CYS A 871 " distance=2.03 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 994 " distance=2.04 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1197 " distance=2.02 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1287 " distance=2.10 Simple disulfide: pdb=" SG CYS B 250 " - pdb=" SG CYS B 254 " distance=2.13 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 444 " distance=2.11 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 626 " distance=2.05 Simple disulfide: pdb=" SG CYS B 581 " - pdb=" SG CYS B 594 " distance=2.07 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 636 " distance=2.04 Simple disulfide: pdb=" SG CYS B 685 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 797 " - pdb=" SG CYS B 809 " distance=2.03 Simple disulfide: pdb=" SG CYS B 860 " - pdb=" SG CYS B 882 " distance=2.16 Simple disulfide: pdb=" SG CYS B 865 " - pdb=" SG CYS B 871 " distance=2.03 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 994 " distance=2.05 Simple disulfide: pdb=" SG CYS B1186 " - pdb=" SG CYS B1197 " distance=2.02 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1287 " distance=2.10 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 254 " distance=2.13 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 444 " distance=2.11 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 492 " distance=2.03 Simple disulfide: pdb=" SG CYS C 567 " - pdb=" SG CYS C 626 " distance=2.05 Simple disulfide: pdb=" SG CYS C 581 " - pdb=" SG CYS C 594 " distance=2.07 Simple disulfide: pdb=" SG CYS C 609 " - pdb=" SG CYS C 636 " distance=2.04 Simple disulfide: pdb=" SG CYS C 685 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 797 " - pdb=" SG CYS C 809 " distance=2.03 Simple disulfide: pdb=" SG CYS C 860 " - pdb=" SG CYS C 882 " distance=2.16 Simple disulfide: pdb=" SG CYS C 865 " - pdb=" SG CYS C 871 " distance=2.03 Simple disulfide: pdb=" SG CYS C 983 " - pdb=" SG CYS C 994 " distance=2.04 Simple disulfide: pdb=" SG CYS C1186 " - pdb=" SG CYS C1197 " distance=2.02 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1287 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A1501 " - " ASN A 531 " " NAG A1502 " - " ASN A 553 " " NAG A1503 " - " ASN A 361 " " NAG A1504 " - " ASN A 515 " " NAG A1505 " - " ASN A1293 " " NAG A1506 " - " ASN A 703 " " NAG A1507 " - " ASN A 779 " " NAG A1508 " - " ASN A 561 " " NAG A1509 " - " ASN A 404 " " NAG A1510 " - " ASN A 818 " " NAG B1501 " - " ASN B 531 " " NAG B1502 " - " ASN B 553 " " NAG B1503 " - " ASN B 361 " " NAG B1504 " - " ASN B 515 " " NAG B1505 " - " ASN B1293 " " NAG B1506 " - " ASN B 703 " " NAG B1507 " - " ASN B 779 " " NAG B1508 " - " ASN B 561 " " NAG B1509 " - " ASN B 404 " " NAG B1510 " - " ASN B 818 " " NAG C1501 " - " ASN C 531 " " NAG C1502 " - " ASN C 553 " " NAG C1503 " - " ASN C 361 " " NAG C1504 " - " ASN C 515 " " NAG C1505 " - " ASN C1293 " " NAG C1506 " - " ASN C 703 " " NAG C1507 " - " ASN C 779 " " NAG C1508 " - " ASN C 561 " " NAG C1509 " - " ASN C 404 " " NAG C1510 " - " ASN C 818 " " NAG D 1 " - " ASN A 448 " " NAG E 1 " - " ASN A 920 " " NAG F 1 " - " ASN A1073 " " NAG G 1 " - " ASN A1199 " " NAG H 1 " - " ASN A 833 " " NAG I 1 " - " ASN A 839 " " NAG J 1 " - " ASN A 284 " " NAG K 1 " - " ASN A 724 " " NAG L 1 " - " ASN A 344 " " NAG M 1 " - " ASN B 448 " " NAG N 1 " - " ASN B 920 " " NAG O 1 " - " ASN B1073 " " NAG P 1 " - " ASN B1199 " " NAG Q 1 " - " ASN B 833 " " NAG R 1 " - " ASN B 839 " " NAG S 1 " - " ASN B 284 " " NAG T 1 " - " ASN B 724 " " NAG U 1 " - " ASN B 344 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 920 " " NAG X 1 " - " ASN C1073 " " NAG Y 1 " - " ASN C1199 " " NAG Z 1 " - " ASN C 833 " " NAG a 1 " - " ASN C 839 " " NAG b 1 " - " ASN C 284 " " NAG c 1 " - " ASN C 724 " " NAG d 1 " - " ASN C 344 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 707.3 milliseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5954 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 39 sheets defined 26.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 34 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.572A pdb=" N VAL A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.506A pdb=" N GLY A 455 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.724A pdb=" N ILE A 490 " --> pdb=" O HIS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 618 removed outlier: 4.027A pdb=" N ASN A 617 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.556A pdb=" N LYS A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 902 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 926 through 930 Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'A' and resid 958 through 968 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 991 through 998 Processing helix chain 'A' and resid 1006 through 1023 Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1037 through 1050 Processing helix chain 'A' and resid 1059 through 1079 Processing helix chain 'A' and resid 1093 through 1119 removed outlier: 3.768A pdb=" N LEU A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A1119 " --> pdb=" O HIS A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1122 No H-bonds generated for 'chain 'A' and resid 1120 through 1122' Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1139 through 1187 removed outlier: 4.508A pdb=" N ALA A1145 " --> pdb=" O PRO A1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1279 No H-bonds generated for 'chain 'A' and resid 1277 through 1279' Processing helix chain 'A' and resid 1298 through 1303 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.572A pdb=" N VAL B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.506A pdb=" N GLY B 455 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.724A pdb=" N ILE B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 618 removed outlier: 4.028A pdb=" N ASN B 617 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 868 through 875 removed outlier: 3.556A pdb=" N LYS B 873 " --> pdb=" O PRO B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 902 Processing helix chain 'B' and resid 908 through 914 Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 926 through 930 Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'B' and resid 958 through 968 Processing helix chain 'B' and resid 980 through 985 Processing helix chain 'B' and resid 991 through 998 Processing helix chain 'B' and resid 1006 through 1023 Processing helix chain 'B' and resid 1024 through 1026 No H-bonds generated for 'chain 'B' and resid 1024 through 1026' Processing helix chain 'B' and resid 1037 through 1050 Processing helix chain 'B' and resid 1059 through 1079 Processing helix chain 'B' and resid 1093 through 1119 removed outlier: 3.768A pdb=" N LEU B1116 " --> pdb=" O ALA B1112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B1119 " --> pdb=" O HIS B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1130 through 1136 Processing helix chain 'B' and resid 1139 through 1187 removed outlier: 4.508A pdb=" N ALA B1145 " --> pdb=" O PRO B1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1279 No H-bonds generated for 'chain 'B' and resid 1277 through 1279' Processing helix chain 'B' and resid 1298 through 1303 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.572A pdb=" N VAL C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.506A pdb=" N GLY C 455 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.723A pdb=" N ILE C 490 " --> pdb=" O HIS C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 618 removed outlier: 4.028A pdb=" N ASN C 617 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 875 removed outlier: 3.556A pdb=" N LYS C 873 " --> pdb=" O PRO C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 902 Processing helix chain 'C' and resid 908 through 914 Processing helix chain 'C' and resid 915 through 920 Processing helix chain 'C' and resid 926 through 930 Processing helix chain 'C' and resid 939 through 944 Processing helix chain 'C' and resid 958 through 968 Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 991 through 998 Processing helix chain 'C' and resid 1006 through 1023 Processing helix chain 'C' and resid 1024 through 1026 No H-bonds generated for 'chain 'C' and resid 1024 through 1026' Processing helix chain 'C' and resid 1037 through 1050 Processing helix chain 'C' and resid 1059 through 1079 Processing helix chain 'C' and resid 1093 through 1119 removed outlier: 3.768A pdb=" N LEU C1116 " --> pdb=" O ALA C1112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C1119 " --> pdb=" O HIS C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1122 No H-bonds generated for 'chain 'C' and resid 1120 through 1122' Processing helix chain 'C' and resid 1130 through 1136 Processing helix chain 'C' and resid 1139 through 1187 removed outlier: 4.508A pdb=" N ALA C1145 " --> pdb=" O PRO C1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C1149 " --> pdb=" O ALA C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1279 No H-bonds generated for 'chain 'C' and resid 1277 through 1279' Processing helix chain 'C' and resid 1298 through 1303 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 307 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 290 through 307 current: chain 'A' and resid 421 through 424 removed outlier: 4.040A pdb=" N HIS A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 437 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A 431 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 434 through 438 current: chain 'A' and resid 477 through 482 Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 318 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 313 through 318 current: chain 'A' and resid 367 through 373 removed outlier: 7.686A pdb=" N CYS A 399 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR A 410 " --> pdb=" O CYS A 399 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 401 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 502 through 507 removed outlier: 3.812A pdb=" N GLY A 751 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 515 through 519 removed outlier: 4.399A pdb=" N ASN A 515 " --> pdb=" O CYS A 685 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU A 720 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 540 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 546 through 548 current: chain 'A' and resid 592 through 593 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 592 through 593 current: chain 'A' and resid 648 through 666 Processing sheet with id=AA8, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.753A pdb=" N VAL A 808 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR A 802 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 820 through 822 removed outlier: 6.416A pdb=" N THR A 820 " --> pdb=" O VAL C 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 833 through 850 removed outlier: 6.493A pdb=" N ASN A 833 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR A1230 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 835 " --> pdb=" O THR A1228 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A1228 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR A1226 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A 839 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY A1213 " --> pdb=" O ALA A1209 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA A1209 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A1215 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A1207 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A1217 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A1205 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A1219 " --> pdb=" O LEU A1203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 856 through 858 Processing sheet with id=AB3, first strand: chain 'A' and resid 905 through 907 Processing sheet with id=AB4, first strand: chain 'A' and resid 1281 through 1284 Processing sheet with id=AB5, first strand: chain 'A' and resid 1253 through 1257 Processing sheet with id=AB6, first strand: chain 'B' and resid 52 through 57 Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 307 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 290 through 307 current: chain 'B' and resid 421 through 424 removed outlier: 4.040A pdb=" N HIS B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 437 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 431 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 434 through 438 current: chain 'B' and resid 477 through 482 Processing sheet with id=AB9, first strand: chain 'B' and resid 313 through 318 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 313 through 318 current: chain 'B' and resid 367 through 373 removed outlier: 7.686A pdb=" N CYS B 399 " --> pdb=" O TYR B 410 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 410 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 401 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 502 through 507 removed outlier: 3.813A pdb=" N GLY B 751 " --> pdb=" O ALA B 743 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 515 through 519 removed outlier: 4.399A pdb=" N ASN B 515 " --> pdb=" O CYS B 685 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU B 720 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 527 through 540 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 546 through 548 current: chain 'B' and resid 592 through 593 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 592 through 593 current: chain 'B' and resid 648 through 666 Processing sheet with id=AC4, first strand: chain 'B' and resid 799 through 803 removed outlier: 6.753A pdb=" N VAL B 808 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR B 802 " --> pdb=" O ILE B 806 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 833 through 850 removed outlier: 6.493A pdb=" N ASN B 833 " --> pdb=" O THR B1230 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B1230 " --> pdb=" O ASN B 833 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 835 " --> pdb=" O THR B1228 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B1228 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR B1226 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B 839 " --> pdb=" O THR B1224 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY B1213 " --> pdb=" O ALA B1209 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B1209 " --> pdb=" O GLY B1213 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B1215 " --> pdb=" O ALA B1207 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B1207 " --> pdb=" O ILE B1215 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B1217 " --> pdb=" O SER B1205 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER B1205 " --> pdb=" O PHE B1217 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR B1219 " --> pdb=" O LEU B1203 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 856 through 858 Processing sheet with id=AC7, first strand: chain 'B' and resid 905 through 907 Processing sheet with id=AC8, first strand: chain 'B' and resid 1281 through 1284 Processing sheet with id=AC9, first strand: chain 'B' and resid 1253 through 1257 Processing sheet with id=AD1, first strand: chain 'C' and resid 52 through 57 Processing sheet with id=AD2, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AD3, first strand: chain 'C' and resid 290 through 307 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 290 through 307 current: chain 'C' and resid 421 through 424 removed outlier: 4.040A pdb=" N HIS C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 437 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 431 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN C 435 " --> pdb=" O ILE C 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 434 through 438 current: chain 'C' and resid 477 through 482 Processing sheet with id=AD4, first strand: chain 'C' and resid 313 through 318 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 318 current: chain 'C' and resid 367 through 373 removed outlier: 7.686A pdb=" N CYS C 399 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR C 410 " --> pdb=" O CYS C 399 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 401 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 502 through 507 removed outlier: 3.812A pdb=" N GLY C 751 " --> pdb=" O ALA C 743 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 515 through 519 removed outlier: 4.399A pdb=" N ASN C 515 " --> pdb=" O CYS C 685 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU C 720 " --> pdb=" O VAL C 733 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 527 through 540 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 546 through 548 current: chain 'C' and resid 592 through 593 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 592 through 593 current: chain 'C' and resid 648 through 666 Processing sheet with id=AD8, first strand: chain 'C' and resid 799 through 803 removed outlier: 6.752A pdb=" N VAL C 808 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR C 802 " --> pdb=" O ILE C 806 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 806 " --> pdb=" O THR C 802 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 833 through 850 removed outlier: 6.493A pdb=" N ASN C 833 " --> pdb=" O THR C1230 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR C1230 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 835 " --> pdb=" O THR C1228 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C1228 " --> pdb=" O THR C 835 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C1226 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN C 839 " --> pdb=" O THR C1224 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY C1213 " --> pdb=" O ALA C1209 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA C1209 " --> pdb=" O GLY C1213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C1215 " --> pdb=" O ALA C1207 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA C1207 " --> pdb=" O ILE C1215 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C1217 " --> pdb=" O SER C1205 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER C1205 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR C1219 " --> pdb=" O LEU C1203 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 856 through 858 Processing sheet with id=AE2, first strand: chain 'C' and resid 1281 through 1284 Processing sheet with id=AE3, first strand: chain 'C' and resid 1253 through 1257 821 hydrogen bonds defined for protein. 2277 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6240 1.33 - 1.47: 7733 1.47 - 1.61: 10641 1.61 - 1.75: 9 1.75 - 1.89: 153 Bond restraints: 24776 Sorted by residual: bond pdb=" C CYS A 865 " pdb=" O CYS A 865 " ideal model delta sigma weight residual 1.234 1.345 -0.110 1.16e-02 7.43e+03 9.04e+01 bond pdb=" C CYS B 865 " pdb=" O CYS B 865 " ideal model delta sigma weight residual 1.234 1.344 -0.110 1.16e-02 7.43e+03 8.98e+01 bond pdb=" C CYS C 865 " pdb=" O CYS C 865 " ideal model delta sigma weight residual 1.234 1.344 -0.110 1.16e-02 7.43e+03 8.96e+01 bond pdb=" C CYS A 865 " pdb=" N ASN A 866 " ideal model delta sigma weight residual 1.334 1.266 0.068 1.25e-02 6.40e+03 2.95e+01 bond pdb=" C CYS B 865 " pdb=" N ASN B 866 " ideal model delta sigma weight residual 1.334 1.266 0.068 1.25e-02 6.40e+03 2.94e+01 ... (remaining 24771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.48: 33767 6.48 - 12.96: 104 12.96 - 19.45: 15 19.45 - 25.93: 3 25.93 - 32.41: 6 Bond angle restraints: 33895 Sorted by residual: angle pdb=" N SER C 584 " pdb=" CA SER C 584 " pdb=" C SER C 584 " ideal model delta sigma weight residual 114.56 146.97 -32.41 1.27e+00 6.20e-01 6.51e+02 angle pdb=" N SER B 584 " pdb=" CA SER B 584 " pdb=" C SER B 584 " ideal model delta sigma weight residual 114.56 146.96 -32.40 1.27e+00 6.20e-01 6.51e+02 angle pdb=" N SER A 584 " pdb=" CA SER A 584 " pdb=" C SER A 584 " ideal model delta sigma weight residual 114.56 146.93 -32.37 1.27e+00 6.20e-01 6.50e+02 angle pdb=" N LEU C 585 " pdb=" CA LEU C 585 " pdb=" CB LEU C 585 " ideal model delta sigma weight residual 110.49 140.89 -30.40 1.69e+00 3.50e-01 3.24e+02 angle pdb=" N LEU A 585 " pdb=" CA LEU A 585 " pdb=" CB LEU A 585 " ideal model delta sigma weight residual 110.49 140.86 -30.37 1.69e+00 3.50e-01 3.23e+02 ... (remaining 33890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 13262 16.95 - 33.90: 464 33.90 - 50.85: 70 50.85 - 67.79: 32 67.79 - 84.74: 10 Dihedral angle restraints: 13838 sinusoidal: 4597 harmonic: 9241 Sorted by residual: dihedral pdb=" N LEU C 585 " pdb=" C LEU C 585 " pdb=" CA LEU C 585 " pdb=" CB LEU C 585 " ideal model delta harmonic sigma weight residual 122.80 149.05 -26.25 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" N LEU A 585 " pdb=" C LEU A 585 " pdb=" CA LEU A 585 " pdb=" CB LEU A 585 " ideal model delta harmonic sigma weight residual 122.80 148.98 -26.18 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" N LEU B 585 " pdb=" C LEU B 585 " pdb=" CA LEU B 585 " pdb=" CB LEU B 585 " ideal model delta harmonic sigma weight residual 122.80 148.97 -26.17 0 2.50e+00 1.60e-01 1.10e+02 ... (remaining 13835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 4231 0.344 - 0.689: 96 0.689 - 1.033: 6 1.033 - 1.377: 3 1.377 - 1.722: 3 Chirality restraints: 4339 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 4336 not shown) Planarity restraints: 4267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " 0.226 2.00e-02 2.50e+03 1.91e-01 4.55e+02 pdb=" C7 NAG S 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " -0.310 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.225 2.00e-02 2.50e+03 1.91e-01 4.55e+02 pdb=" C7 NAG J 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.310 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " 0.225 2.00e-02 2.50e+03 1.91e-01 4.54e+02 pdb=" C7 NAG b 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " -0.310 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " 0.175 2.00e-02 2.50e+03 ... (remaining 4264 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 52 2.55 - 3.14: 18892 3.14 - 3.73: 34829 3.73 - 4.31: 53829 4.31 - 4.90: 84693 Nonbonded interactions: 192295 Sorted by model distance: nonbonded pdb=" OG SER B 541 " pdb=" OD2 ASP C 560 " model vdw 1.968 3.040 nonbonded pdb=" CE2 TYR C 235 " pdb=" CZ PHE C 457 " model vdw 2.262 3.640 nonbonded pdb=" CE2 TYR A 235 " pdb=" CZ PHE A 457 " model vdw 2.263 3.640 nonbonded pdb=" CE2 TYR B 235 " pdb=" CZ PHE B 457 " model vdw 2.263 3.640 nonbonded pdb=" N SER B 541 " pdb=" O SER B 541 " model vdw 2.427 2.496 ... (remaining 192290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 34 through 47 and (name N or name CA or name C or name O \ or name CB )) or resid 48 through 52 or (resid 53 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 180 or (resid 181 thro \ ugh 185 and (name N or name CA or name C or name O or name CB )) or resid 193 th \ rough 203 or resid 232 through 237 or (resid 238 through 249 and (name N or name \ CA or name C or name O or name CB )) or resid 250 through 272 or (resid 273 and \ (name N or name CA or name C or name O or name CB )) or resid 274 through 497 o \ r (resid 498 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 99 through 546 or (resid 547 through 548 and (name N or name CA or name C or nam \ e O or name CB )) or resid 549 through 550 or (resid 551 and (name N or name CA \ or name C or name O or name CB )) or resid 552 through 648 or (resid 649 and (na \ me N or name CA or name C or name O or name CB )) or resid 650 through 869 or (r \ esid 870 and (name N or name CA or name C or name O or name CB )) or resid 871 t \ hrough 872 or (resid 873 and (name N or name CA or name C or name O or name CB ) \ ) or resid 874 through 876 or (resid 877 and (name N or name CA or name C or nam \ e O or name CB )) or resid 878 through 885 or (resid 886 and (name N or name CA \ or name C or name O or name CB )) or resid 887 through 922 or (resid 923 and (na \ me N or name CA or name C or name O or name CB )) or resid 924 through 987 or (r \ esid 988 and (name N or name CA or name C or name O or name CB )) or resid 989 t \ hrough 1055 or (resid 1056 through 1059 and (name N or name CA or name C or name \ O or name CB )) or resid 1060 through 1100 or (resid 1101 and (name N or name C \ A or name C or name O or name CB )) or resid 1102 or (resid 1103 and (name N or \ name CA or name C or name O or name CB )) or resid 1104 through 1110 or (resid 1 \ 111 through 1112 and (name N or name CA or name C or name O or name CB )) or res \ id 1113 through 1124 or (resid 1125 through 1126 and (name N or name CA or name \ C or name O or name CB )) or resid 1127 through 1132 or (resid 1133 and (name N \ or name CA or name C or name O or name CB )) or resid 1134 through 1138 or (resi \ d 1139 and (name N or name CA or name C or name O or name CB )) or resid 1140 th \ rough 1147 or (resid 1148 and (name N or name CA or name C or name O or name CB \ )) or resid 1149 through 1163 or (resid 1164 and (name N or name CA or name C or \ name O or name CB )) or resid 1165 through 1170 or (resid 1171 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1172 through 1259 or (resid 12 \ 60 through 1262 and (name N or name CA or name C or name O or name CB )) or resi \ d 1263 through 1287 or (resid 1288 through 1290 and (name N or name CA or name C \ or name O or name CB )) or resid 1291 through 1294 or (resid 1295 through 1299 \ and (name N or name CA or name C or name O or name CB )) or resid 1300 through 1 \ 301 or (resid 1302 through 1303 and (name N or name CA or name C or name O or na \ me CB )) or resid 1501 through 1510)) selection = (chain 'B' and ((resid 34 through 47 and (name N or name CA or name C or name O \ or name CB )) or resid 48 through 200 or (resid 201 through 202 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 203 through 234 and (name N o \ r name CA or name C or name O or name CB )) or resid 235 through 239 or (resid 2 \ 40 through 249 and (name N or name CA or name C or name O or name CB )) or resid \ 250 through 262 or (resid 263 and (name N or name CA or name C or name O or nam \ e CB )) or resid 264 through 272 or (resid 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 308 or (resid 309 and (name N or na \ me CA or name C or name O or name CB )) or resid 310 through 314 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 through 325 \ or (resid 326 and (name N or name CA or name C or name O or name CB )) or resid \ 327 or (resid 328 through 330 and (name N or name CA or name C or name O or nam \ e CB )) or resid 331 through 332 or (resid 333 through 334 and (name N or name C \ A or name C or name O or name CB )) or resid 335 through 347 or (resid 348 and ( \ name N or name CA or name C or name O or name CB )) or resid 349 or (resid 350 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 362 \ or (resid 363 and (name N or name CA or name C or name O or name CB )) or resid \ 364 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 through 538 or (resid 539 through 541 and (name N or name C \ A or name C or name O or name CB )) or resid 542 through 587 or (resid 588 throu \ gh 589 and (name N or name CA or name C or name O or name CB )) or resid 590 or \ (resid 591 through 593 and (name N or name CA or name C or name O or name CB )) \ or resid 594 through 596 or (resid 597 and (name N or name CA or name C or name \ O or name CB )) or resid 598 through 627 or (resid 628 and (name N or name CA or \ name C or name O or name CB )) or resid 629 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 638 or (res \ id 639 and (name N or name CA or name C or name O or name CB )) or resid 640 thr \ ough 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) \ or resid 650 through 662 or (resid 663 and (name N or name CA or name C or name \ O or name CB )) or resid 664 through 677 or (resid 678 and (name N or name CA or \ name C or name O or name CB )) or resid 679 through 682 or (resid 683 and (name \ N or name CA or name C or name O or name CB )) or resid 684 through 686 or (res \ id 687 and (name N or name CA or name C or name O or name CB )) or resid 688 thr \ ough 736 or (resid 737 and (name N or name CA or name C or name O or name CB )) \ or resid 738 through 745 or (resid 746 and (name N or name CA or name C or name \ O or name CB )) or resid 747 through 876 or (resid 877 and (name N or name CA or \ name C or name O or name CB )) or resid 878 through 885 or (resid 886 and (name \ N or name CA or name C or name O or name CB )) or resid 887 through 965 or (res \ id 966 and (name N or name CA or name C or name O or name CB )) or resid 967 thr \ ough 1009 or (resid 1010 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1011 through 1055 or (resid 1056 through 1059 and (name N or name CA \ or name C or name O or name CB )) or resid 1060 through 1108 or (resid 1109 and \ (name N or name CA or name C or name O or name CB )) or resid 1110 through 1147 \ or (resid 1148 and (name N or name CA or name C or name O or name CB )) or resid \ 1149 through 1510)) selection = (chain 'C' and ((resid 34 through 47 and (name N or name CA or name C or name O \ or name CB )) or resid 48 through 185 or (resid 193 through 202 and (name N or n \ ame CA or name C or name O or name CB )) or resid 203 or resid 232 through 308 o \ r (resid 309 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 10 through 314 or (resid 315 and (name N or name CA or name C or name O or name \ CB )) or resid 316 through 327 or (resid 328 through 330 and (name N or name CA \ or name C or name O or name CB )) or resid 331 through 332 or (resid 333 through \ 334 and (name N or name CA or name C or name O or name CB )) or resid 335 throu \ gh 347 or (resid 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 or (resid 350 and (name N or name CA or name C or name O or name CB ) \ ) or resid 351 through 362 or (resid 363 and (name N or name CA or name C or nam \ e O or name CB )) or resid 364 through 442 or (resid 443 and (name N or name CA \ or name C or name O or name CB )) or resid 444 through 466 or (resid 467 through \ 468 and (name N or name CA or name C or name O or name CB )) or resid 469 throu \ gh 534 or (resid 535 and (name N or name CA or name C or name O or name CB )) or \ resid 536 through 539 or (resid 540 through 541 and (name N or name CA or name \ C or name O or name CB )) or resid 542 through 546 or (resid 547 through 548 and \ (name N or name CA or name C or name O or name CB )) or resid 549 through 550 o \ r (resid 551 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 52 through 559 or (resid 560 and (name N or name CA or name C or name O or name \ CB )) or resid 561 through 563 or (resid 564 and (name N or name CA or name C or \ name O or name CB )) or resid 565 through 578 or (resid 579 and (name N or name \ CA or name C or name O or name CB )) or resid 580 through 613 or (resid 614 and \ (name N or name CA or name C or name O or name CB )) or resid 615 through 627 o \ r (resid 628 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 29 through 631 or (resid 632 and (name N or name CA or name C or name O or name \ CB )) or resid 633 through 662 or (resid 663 and (name N or name CA or name C or \ name O or name CB )) or resid 664 through 669 or (resid 677 through 678 and (na \ me N or name CA or name C or name O or name CB )) or resid 679 through 682 or (r \ esid 683 and (name N or name CA or name C or name O or name CB )) or resid 684 t \ hrough 686 or (resid 687 and (name N or name CA or name C or name O or name CB ) \ ) or resid 688 through 736 or (resid 737 and (name N or name CA or name C or nam \ e O or name CB )) or resid 738 through 745 or (resid 746 and (name N or name CA \ or name C or name O or name CB )) or resid 747 through 922 or (resid 923 and (na \ me N or name CA or name C or name O or name CB )) or resid 924 through 1102 or ( \ resid 1103 and (name N or name CA or name C or name O or name CB )) or resid 110 \ 4 through 1110 or (resid 1111 through 1112 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1113 through 1287 or (resid 1288 through 1290 and ( \ name N or name CA or name C or name O or name CB )) or resid 1291 through 1294 o \ r (resid 1295 through 1299 and (name N or name CA or name C or name O or name CB \ )) or resid 1300 through 1510)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'S' selection = chain 'U' selection = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.320 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: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.240 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.015 0.130 24911 Z= 0.840 Angle : 1.665 32.410 34255 Z= 1.045 Chirality : 0.130 1.722 4339 Planarity : 0.010 0.191 4210 Dihedral : 9.682 84.742 7749 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.50 % Favored : 96.21 % Rotamer: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.43 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.14), residues: 3115 helix: 0.36 (0.17), residues: 705 sheet: 0.69 (0.17), residues: 783 loop : -0.31 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 397 TYR 0.046 0.006 TYR A1016 PHE 0.022 0.003 PHE C 524 TRP 0.032 0.007 TRP C 458 HIS 0.005 0.001 HIS A1202 Details of bonding type rmsd/Z covalent geometry : bond 0.01462 / 0.81 (24776) covalent geometry : angle 1.60025 / 1.04 (33895) SS BOND : bond 0.05166 / 3.92 ( 45) SS BOND : angle 3.86816 / 2.81 ( 90) hydrogen bonds : bond 0.19260 / 13.32 ( 821) hydrogen bonds : angle 6.74963 / 4.70 ( 2277) link_BETA1-4 : bond 0.05825 / 4.32 ( 33) link_BETA1-4 : angle 4.55303 / 3.34 ( 99) link_NAG-ASN : bond 0.07256 / 5.23 ( 57) link_NAG-ASN : angle 5.30907 / 3.69 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 0.587 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 392 average time/residue: 0.4911 time to fit residues: 227.1686 Evaluate side-chains 217 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 619 HIS A1076 GLN A1103 GLN A1107 ASN A1122 ASN A1208 ASN B 527 HIS B 578 HIS B 619 HIS B1107 ASN B1109 GLN B1122 ASN B1208 ASN C 527 HIS C 578 HIS C 619 HIS C1076 GLN C1103 GLN C1107 ASN C1122 ASN C1208 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.106713 restraints weight = 28723.193| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.38 r_work: 0.2912 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24911 Z= 0.169 Angle : 0.723 21.740 34255 Z= 0.351 Chirality : 0.050 0.542 4339 Planarity : 0.004 0.042 4210 Dihedral : 4.631 23.747 3363 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.01 % Rotamer: Outliers : 2.70 % Allowed : 6.59 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 3115 helix: 1.72 (0.19), residues: 711 sheet: 0.60 (0.18), residues: 755 loop : -0.21 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1149 TYR 0.022 0.002 TYR C1016 PHE 0.017 0.002 PHE A 638 TRP 0.017 0.002 TRP C 458 HIS 0.004 0.001 HIS B 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (24776) covalent geometry : angle 0.63864 / 0.33 (33895) SS BOND : bond 0.00388 / 0.27 ( 45) SS BOND : angle 1.45470 / 0.97 ( 90) hydrogen bonds : bond 0.06991 / 4.75 ( 821) hydrogen bonds : angle 5.10623 / 3.56 ( 2277) link_BETA1-4 : bond 0.00595 / 0.45 ( 33) link_BETA1-4 : angle 2.30506 / 1.76 ( 99) link_NAG-ASN : bond 0.01011 / 0.69 ( 57) link_NAG-ASN : angle 4.43531 / 3.11 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 256 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.7725 (tp) cc_final: 0.7472 (tp) REVERT: A 471 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: A 576 TYR cc_start: 0.8974 (m-80) cc_final: 0.8629 (m-80) REVERT: A 956 TYR cc_start: 0.6749 (t80) cc_final: 0.6494 (t80) REVERT: A 988 ASP cc_start: 0.8252 (t0) cc_final: 0.7991 (p0) REVERT: A 1103 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7837 (tp-100) REVERT: A 1111 GLN cc_start: 0.8611 (mt0) cc_final: 0.8376 (mt0) REVERT: A 1149 ARG cc_start: 0.8295 (mtt90) cc_final: 0.8016 (mtt-85) REVERT: B 478 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8318 (mtpp) REVERT: B 647 ASN cc_start: 0.7303 (t0) cc_final: 0.6683 (p0) REVERT: B 1185 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8590 (mt-10) REVERT: C 471 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: C 478 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8241 (mtpp) REVERT: C 647 ASN cc_start: 0.7346 (t0) cc_final: 0.6853 (p0) REVERT: C 956 TYR cc_start: 0.6855 (t80) cc_final: 0.6591 (t80) REVERT: C 1103 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7857 (tp-100) outliers start: 62 outliers final: 22 residues processed: 289 average time/residue: 0.4406 time to fit residues: 153.5330 Evaluate side-chains 237 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1103 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 241 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 209 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 113 optimal weight: 0.0040 chunk 153 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A1103 GLN B 578 HIS C 302 ASN C 474 ASN C 578 HIS C1103 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.106591 restraints weight = 28781.945| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.36 r_work: 0.2908 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24911 Z= 0.146 Angle : 0.654 17.197 34255 Z= 0.313 Chirality : 0.047 0.406 4339 Planarity : 0.004 0.042 4210 Dihedral : 4.418 19.284 3361 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.30 % Rotamer: Outliers : 2.66 % Allowed : 7.89 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3115 helix: 2.01 (0.19), residues: 729 sheet: 0.47 (0.18), residues: 728 loop : -0.23 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 340 TYR 0.020 0.001 TYR C1016 PHE 0.013 0.001 PHE A 457 TRP 0.010 0.001 TRP C 458 HIS 0.003 0.001 HIS C 821 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24776) covalent geometry : angle 0.56643 / 0.29 (33895) SS BOND : bond 0.00534 / 0.35 ( 45) SS BOND : angle 2.06882 / 1.45 ( 90) hydrogen bonds : bond 0.06245 / 4.24 ( 821) hydrogen bonds : angle 4.68976 / 3.26 ( 2277) link_BETA1-4 : bond 0.00477 / 0.36 ( 33) link_BETA1-4 : angle 1.73102 / 1.31 ( 99) link_NAG-ASN : bond 0.00864 / 0.59 ( 57) link_NAG-ASN : angle 4.23991 / 3.05 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 1.029 Fit side-chains REVERT: A 414 LEU cc_start: 0.7724 (tp) cc_final: 0.7424 (tp) REVERT: A 471 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: A 576 TYR cc_start: 0.9031 (m-80) cc_final: 0.8680 (m-80) REVERT: A 956 TYR cc_start: 0.6764 (t80) cc_final: 0.6504 (t80) REVERT: A 988 ASP cc_start: 0.8310 (t0) cc_final: 0.8096 (p0) REVERT: A 1103 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8093 (tp-100) REVERT: A 1111 GLN cc_start: 0.8654 (mt0) cc_final: 0.8414 (mt0) REVERT: A 1149 ARG cc_start: 0.8268 (mtt90) cc_final: 0.8067 (mtt-85) REVERT: B 425 LYS cc_start: 0.8552 (pttp) cc_final: 0.8304 (ptpp) REVERT: B 471 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8285 (tm-30) REVERT: B 478 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8395 (mtpp) REVERT: B 647 ASN cc_start: 0.7339 (t0) cc_final: 0.6731 (p0) REVERT: B 1104 ASP cc_start: 0.8726 (t0) cc_final: 0.8493 (t0) REVERT: B 1185 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: C 471 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: C 478 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8250 (mtpp) REVERT: C 647 ASN cc_start: 0.7425 (t0) cc_final: 0.6891 (p0) REVERT: C 887 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8449 (tt0) REVERT: C 956 TYR cc_start: 0.6894 (t80) cc_final: 0.6673 (t80) REVERT: C 1103 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8128 (tp-100) outliers start: 61 outliers final: 27 residues processed: 269 average time/residue: 0.4637 time to fit residues: 150.6978 Evaluate side-chains 239 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 151 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 290 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 649 GLN A1103 GLN A1122 ASN A1258 ASN B 302 ASN B1122 ASN C 474 ASN C1103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.137124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101836 restraints weight = 28720.050| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.34 r_work: 0.2813 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24911 Z= 0.270 Angle : 0.804 25.359 34255 Z= 0.386 Chirality : 0.053 0.408 4339 Planarity : 0.005 0.046 4210 Dihedral : 4.897 31.615 3361 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.18 % Favored : 97.69 % Rotamer: Outliers : 3.49 % Allowed : 8.07 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3115 helix: 1.87 (0.20), residues: 714 sheet: 0.49 (0.19), residues: 666 loop : -0.63 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 340 TYR 0.024 0.002 TYR C1016 PHE 0.013 0.002 PHE C1256 TRP 0.011 0.002 TRP A 426 HIS 0.006 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (24776) covalent geometry : angle 0.71588 / 0.36 (33895) SS BOND : bond 0.01096 / 0.70 ( 45) SS BOND : angle 3.39687 / 2.32 ( 90) hydrogen bonds : bond 0.07558 / 5.14 ( 821) hydrogen bonds : angle 4.83566 / 3.36 ( 2277) link_BETA1-4 : bond 0.00365 / 0.27 ( 33) link_BETA1-4 : angle 1.83625 / 1.41 ( 99) link_NAG-ASN : bond 0.00704 / 0.49 ( 57) link_NAG-ASN : angle 4.45427 / 3.25 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 222 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: A 317 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7552 (t80) REVERT: A 414 LEU cc_start: 0.7669 (tp) cc_final: 0.7425 (tp) REVERT: A 471 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: A 576 TYR cc_start: 0.9075 (m-80) cc_final: 0.8736 (m-80) REVERT: A 753 MET cc_start: 0.9215 (mpt) cc_final: 0.8893 (mpt) REVERT: A 988 ASP cc_start: 0.8386 (t0) cc_final: 0.8180 (t0) REVERT: A 1149 ARG cc_start: 0.8380 (mtt90) cc_final: 0.8099 (mtt-85) REVERT: A 1222 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9168 (tp) REVERT: A 1257 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8442 (ttt-90) REVERT: B 317 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (t80) REVERT: B 425 LYS cc_start: 0.8647 (pttp) cc_final: 0.8354 (ptpp) REVERT: B 471 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: B 647 ASN cc_start: 0.7305 (t0) cc_final: 0.6566 (p0) REVERT: B 1185 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.8803 (mt-10) REVERT: C 317 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7918 (t80) REVERT: C 471 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: C 478 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8208 (mtpp) REVERT: C 647 ASN cc_start: 0.7355 (t0) cc_final: 0.6743 (p0) REVERT: C 887 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: C 956 TYR cc_start: 0.6929 (t80) cc_final: 0.6724 (t80) outliers start: 80 outliers final: 40 residues processed: 273 average time/residue: 0.4131 time to fit residues: 136.7266 Evaluate side-chains 252 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 100 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 866 ASN A1103 GLN A1122 ASN B 866 ASN C 866 ASN C1103 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.101217 restraints weight = 28706.864| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.34 r_work: 0.2816 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9036 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24911 Z= 0.221 Angle : 0.746 19.943 34255 Z= 0.358 Chirality : 0.051 0.439 4339 Planarity : 0.005 0.047 4210 Dihedral : 4.777 30.240 3361 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % Rotamer: Outliers : 3.01 % Allowed : 9.03 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3115 helix: 1.89 (0.20), residues: 714 sheet: 0.40 (0.19), residues: 674 loop : -0.70 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1149 TYR 0.021 0.002 TYR C1016 PHE 0.012 0.002 PHE B1256 TRP 0.009 0.001 TRP A 426 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (24776) covalent geometry : angle 0.65164 / 0.33 (33895) SS BOND : bond 0.00698 / 0.45 ( 45) SS BOND : angle 3.25091 / 2.20 ( 90) hydrogen bonds : bond 0.06977 / 4.74 ( 821) hydrogen bonds : angle 4.68949 / 3.26 ( 2277) link_BETA1-4 : bond 0.00344 / 0.26 ( 33) link_BETA1-4 : angle 1.66931 / 1.28 ( 99) link_NAG-ASN : bond 0.00507 / 0.37 ( 57) link_NAG-ASN : angle 4.50146 / 3.25 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 317 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7654 (t80) REVERT: A 471 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: A 576 TYR cc_start: 0.9062 (m-80) cc_final: 0.8713 (m-80) REVERT: A 753 MET cc_start: 0.9200 (mpt) cc_final: 0.8910 (mpt) REVERT: A 1103 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7924 (tp-100) REVERT: A 1149 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8116 (mtt-85) REVERT: A 1257 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8412 (ttt-90) REVERT: B 317 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.8020 (t80) REVERT: B 425 LYS cc_start: 0.8699 (pttp) cc_final: 0.8417 (ptpp) REVERT: B 471 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: B 478 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8388 (mtpp) REVERT: B 647 ASN cc_start: 0.7321 (t0) cc_final: 0.6543 (p0) REVERT: B 1185 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8767 (mt-10) REVERT: C 317 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7937 (t80) REVERT: C 443 ASP cc_start: 0.7535 (m-30) cc_final: 0.7196 (m-30) REVERT: C 471 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: C 478 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: C 647 ASN cc_start: 0.7318 (t0) cc_final: 0.6705 (p0) REVERT: C 779 ASN cc_start: 0.8449 (m110) cc_final: 0.7927 (m-40) REVERT: C 887 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8394 (tt0) REVERT: C 1103 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7909 (tp-100) outliers start: 69 outliers final: 38 residues processed: 253 average time/residue: 0.4357 time to fit residues: 133.8580 Evaluate side-chains 246 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 195 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 291 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 277 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 649 GLN A 866 ASN A1122 ASN B 866 ASN B1122 ASN C 866 ASN C1122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.139040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104425 restraints weight = 28725.910| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.31 r_work: 0.2841 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24911 Z= 0.143 Angle : 0.675 16.584 34255 Z= 0.323 Chirality : 0.048 0.353 4339 Planarity : 0.004 0.046 4210 Dihedral : 4.601 26.284 3361 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 2.83 % Allowed : 9.77 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.15), residues: 3115 helix: 2.10 (0.20), residues: 714 sheet: 0.40 (0.19), residues: 676 loop : -0.65 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1149 TYR 0.026 0.001 TYR B 778 PHE 0.013 0.001 PHE C 457 TRP 0.013 0.001 TRP C 201 HIS 0.004 0.001 HIS B 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24776) covalent geometry : angle 0.57536 / 0.30 (33895) SS BOND : bond 0.00460 / 0.31 ( 45) SS BOND : angle 2.75819 / 1.81 ( 90) hydrogen bonds : bond 0.06069 / 4.12 ( 821) hydrogen bonds : angle 4.51769 / 3.13 ( 2277) link_BETA1-4 : bond 0.00362 / 0.27 ( 33) link_BETA1-4 : angle 1.50808 / 1.15 ( 99) link_NAG-ASN : bond 0.00711 / 0.47 ( 57) link_NAG-ASN : angle 4.50593 / 3.30 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 206 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 317 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7670 (t80) REVERT: A 471 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 576 TYR cc_start: 0.9075 (m-80) cc_final: 0.8733 (m-80) REVERT: A 703 ASN cc_start: 0.7398 (p0) cc_final: 0.7029 (p0) REVERT: A 753 MET cc_start: 0.9171 (mpt) cc_final: 0.8940 (mpt) REVERT: A 1103 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7855 (tp-100) REVERT: A 1149 ARG cc_start: 0.8330 (mtt90) cc_final: 0.8059 (mtt-85) REVERT: B 471 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: B 478 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8460 (mtpp) REVERT: B 1185 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8740 (mt-10) REVERT: C 317 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7863 (t80) REVERT: C 443 ASP cc_start: 0.7472 (m-30) cc_final: 0.7065 (m-30) REVERT: C 471 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: C 478 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8303 (mtpp) REVERT: C 647 ASN cc_start: 0.7389 (t0) cc_final: 0.6776 (p0) REVERT: C 703 ASN cc_start: 0.7716 (t0) cc_final: 0.7404 (t0) REVERT: C 779 ASN cc_start: 0.8417 (m110) cc_final: 0.7789 (m-40) REVERT: C 887 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: C 1103 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7831 (tp-100) outliers start: 65 outliers final: 33 residues processed: 243 average time/residue: 0.4291 time to fit residues: 127.0068 Evaluate side-chains 243 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 199 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 75 optimal weight: 0.0010 chunk 9 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 132 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 635 ASN A 649 GLN A 866 ASN A1103 GLN B 866 ASN B1122 ASN C 866 ASN C1103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103973 restraints weight = 28653.558| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.31 r_work: 0.2903 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24911 Z= 0.115 Angle : 0.651 19.911 34255 Z= 0.311 Chirality : 0.047 0.618 4339 Planarity : 0.004 0.046 4210 Dihedral : 4.414 34.095 3361 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.61 % Favored : 98.30 % Rotamer: Outliers : 2.05 % Allowed : 10.77 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.15), residues: 3115 helix: 2.24 (0.20), residues: 718 sheet: 0.54 (0.19), residues: 740 loop : -0.58 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1149 TYR 0.027 0.001 TYR A 778 PHE 0.013 0.001 PHE A 457 TRP 0.016 0.001 TRP B 201 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (24776) covalent geometry : angle 0.55815 / 0.29 (33895) SS BOND : bond 0.00428 / 0.27 ( 45) SS BOND : angle 3.21945 / 2.17 ( 90) hydrogen bonds : bond 0.05355 / 3.63 ( 821) hydrogen bonds : angle 4.33003 / 3.00 ( 2277) link_BETA1-4 : bond 0.00384 / 0.29 ( 33) link_BETA1-4 : angle 1.40063 / 1.07 ( 99) link_NAG-ASN : bond 0.00694 / 0.53 ( 57) link_NAG-ASN : angle 4.06990 / 3.07 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 317 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7335 (t80) REVERT: A 471 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 576 TYR cc_start: 0.9107 (m-80) cc_final: 0.8755 (m-80) REVERT: A 703 ASN cc_start: 0.7565 (p0) cc_final: 0.7239 (p0) REVERT: A 956 TYR cc_start: 0.6787 (t80) cc_final: 0.6513 (t80) REVERT: A 1103 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8128 (tp-100) REVERT: A 1222 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9053 (tp) REVERT: B 471 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: B 478 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8411 (mtpp) REVERT: B 1185 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8728 (mt-10) REVERT: C 478 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8275 (mtpp) REVERT: C 647 ASN cc_start: 0.7510 (t0) cc_final: 0.6932 (p0) REVERT: C 703 ASN cc_start: 0.7602 (t0) cc_final: 0.7368 (t0) REVERT: C 779 ASN cc_start: 0.8528 (m110) cc_final: 0.7840 (m-40) REVERT: C 956 TYR cc_start: 0.6923 (t80) cc_final: 0.6716 (t80) REVERT: C 1103 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8074 (tp-100) outliers start: 47 outliers final: 27 residues processed: 237 average time/residue: 0.4323 time to fit residues: 124.2611 Evaluate side-chains 239 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 649 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 242 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 220 optimal weight: 0.0770 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A1103 GLN A1122 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN C 302 ASN C 635 ASN C 866 ASN C1103 GLN C1122 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.103229 restraints weight = 27214.501| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.28 r_work: 0.2871 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24911 Z= 0.165 Angle : 0.671 18.005 34255 Z= 0.322 Chirality : 0.048 0.393 4339 Planarity : 0.004 0.047 4210 Dihedral : 4.543 32.603 3361 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.98 % Rotamer: Outliers : 2.31 % Allowed : 10.82 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3115 helix: 2.20 (0.20), residues: 714 sheet: 0.38 (0.19), residues: 688 loop : -0.61 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1149 TYR 0.024 0.002 TYR B 400 PHE 0.015 0.001 PHE C 324 TRP 0.009 0.001 TRP C 201 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (24776) covalent geometry : angle 0.57926 / 0.30 (33895) SS BOND : bond 0.00449 / 0.30 ( 45) SS BOND : angle 2.96348 / 2.01 ( 90) hydrogen bonds : bond 0.05967 / 4.06 ( 821) hydrogen bonds : angle 4.39324 / 3.04 ( 2277) link_BETA1-4 : bond 0.00349 / 0.26 ( 33) link_BETA1-4 : angle 1.49474 / 1.15 ( 99) link_NAG-ASN : bond 0.00683 / 0.48 ( 57) link_NAG-ASN : angle 4.21125 / 3.04 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 317 PHE cc_start: 0.7688 (OUTLIER) cc_final: 0.7430 (t80) REVERT: A 471 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: A 576 TYR cc_start: 0.9073 (m-80) cc_final: 0.8742 (m-80) REVERT: A 1103 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8110 (tp-100) REVERT: A 1222 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9081 (tp) REVERT: B 471 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: B 478 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8404 (mtpp) REVERT: B 1185 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8712 (mt-10) REVERT: C 443 ASP cc_start: 0.7314 (m-30) cc_final: 0.6981 (m-30) REVERT: C 471 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: C 478 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8344 (mtpp) REVERT: C 647 ASN cc_start: 0.7545 (t0) cc_final: 0.6978 (p0) REVERT: C 703 ASN cc_start: 0.7812 (t0) cc_final: 0.7594 (t0) REVERT: C 779 ASN cc_start: 0.8550 (m110) cc_final: 0.7870 (m-40) REVERT: C 887 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: C 956 TYR cc_start: 0.6972 (t80) cc_final: 0.6743 (t80) REVERT: C 1103 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8145 (tp-100) outliers start: 53 outliers final: 33 residues processed: 243 average time/residue: 0.4095 time to fit residues: 121.0730 Evaluate side-chains 242 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 112 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 262 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 287 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN A 866 ASN A1103 GLN A1122 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN B1122 ASN C 302 ASN C 866 ASN C1103 GLN C1122 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.139451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.102455 restraints weight = 27256.608| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.24 r_work: 0.2849 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9081 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24911 Z= 0.146 Angle : 0.668 19.461 34255 Z= 0.321 Chirality : 0.049 0.857 4339 Planarity : 0.004 0.047 4210 Dihedral : 4.503 32.104 3361 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.70 % Favored : 98.20 % Rotamer: Outliers : 2.05 % Allowed : 11.12 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.15), residues: 3115 helix: 2.23 (0.20), residues: 714 sheet: 0.36 (0.19), residues: 686 loop : -0.61 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1149 TYR 0.020 0.001 TYR B 400 PHE 0.015 0.001 PHE C 324 TRP 0.011 0.001 TRP B 201 HIS 0.004 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (24776) covalent geometry : angle 0.57940 / 0.30 (33895) SS BOND : bond 0.00445 / 0.29 ( 45) SS BOND : angle 3.30840 / 2.16 ( 90) hydrogen bonds : bond 0.05822 / 3.95 ( 821) hydrogen bonds : angle 4.36083 / 3.02 ( 2277) link_BETA1-4 : bond 0.00360 / 0.27 ( 33) link_BETA1-4 : angle 1.46489 / 1.12 ( 99) link_NAG-ASN : bond 0.00514 / 0.38 ( 57) link_NAG-ASN : angle 3.98937 / 2.81 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.734 Fit side-chains REVERT: A 471 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: A 495 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9019 (mt) REVERT: A 576 TYR cc_start: 0.9087 (m-80) cc_final: 0.8749 (m-80) REVERT: A 1103 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8030 (tp-100) REVERT: A 1222 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9072 (tp) REVERT: B 471 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8258 (tm-30) REVERT: B 478 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8441 (mtpp) REVERT: B 1185 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8744 (mt-10) REVERT: C 345 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.8077 (m-80) REVERT: C 471 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: C 478 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8332 (mtpp) REVERT: C 647 ASN cc_start: 0.7545 (t0) cc_final: 0.6988 (p0) REVERT: C 703 ASN cc_start: 0.7865 (t0) cc_final: 0.7637 (t0) REVERT: C 779 ASN cc_start: 0.8546 (m110) cc_final: 0.7883 (m-40) REVERT: C 887 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: C 956 TYR cc_start: 0.6978 (t80) cc_final: 0.6738 (t80) REVERT: C 1103 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8067 (tp-100) outliers start: 47 outliers final: 31 residues processed: 230 average time/residue: 0.4496 time to fit residues: 124.9410 Evaluate side-chains 234 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 345 PHE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 180 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 310 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 GLN A1103 GLN A1122 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN B1122 ASN C 302 ASN C 635 ASN C 866 ASN C1103 GLN C1122 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.139064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103578 restraints weight = 27368.405| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.30 r_work: 0.2860 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24911 Z= 0.167 Angle : 0.720 26.410 34255 Z= 0.337 Chirality : 0.049 0.611 4339 Planarity : 0.004 0.047 4210 Dihedral : 4.603 32.181 3361 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.95 % Rotamer: Outliers : 2.09 % Allowed : 11.08 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.15), residues: 3115 helix: 2.18 (0.20), residues: 714 sheet: 0.36 (0.19), residues: 675 loop : -0.64 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1149 TYR 0.025 0.002 TYR B 400 PHE 0.016 0.001 PHE C 324 TRP 0.011 0.001 TRP B 201 HIS 0.004 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (24776) covalent geometry : angle 0.59778 / 0.31 (33895) SS BOND : bond 0.00412 / 0.28 ( 45) SS BOND : angle 3.10822 / 2.04 ( 90) hydrogen bonds : bond 0.06045 / 4.11 ( 821) hydrogen bonds : angle 4.39854 / 3.04 ( 2277) link_BETA1-4 : bond 0.00343 / 0.26 ( 33) link_BETA1-4 : angle 1.48737 / 1.14 ( 99) link_NAG-ASN : bond 0.00603 / 0.44 ( 57) link_NAG-ASN : angle 5.17463 / 3.55 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.764 Fit side-chains REVERT: A 471 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: A 495 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9000 (mt) REVERT: A 576 TYR cc_start: 0.9076 (m-80) cc_final: 0.8744 (m-80) REVERT: A 1222 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9093 (tp) REVERT: B 471 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: B 478 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8411 (mtpp) REVERT: B 1185 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8730 (mt-10) REVERT: C 471 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: C 478 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8341 (mtpp) REVERT: C 647 ASN cc_start: 0.7503 (t0) cc_final: 0.6970 (p0) REVERT: C 703 ASN cc_start: 0.7939 (t0) cc_final: 0.7727 (t0) REVERT: C 779 ASN cc_start: 0.8507 (m110) cc_final: 0.7845 (m-40) REVERT: C 887 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: C 956 TYR cc_start: 0.6915 (t80) cc_final: 0.6656 (t80) REVERT: C 1103 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8007 (tp-100) outliers start: 48 outliers final: 33 residues processed: 229 average time/residue: 0.4101 time to fit residues: 113.7778 Evaluate side-chains 231 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1222 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 887 GLN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 1103 GLN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 110 optimal weight: 1.9990 chunk 178 optimal weight: 0.0980 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1103 GLN A1122 ASN ** B 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN C 302 ASN C 866 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103054 restraints weight = 27265.037| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.27 r_work: 0.2859 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24911 Z= 0.132 Angle : 0.652 20.915 34255 Z= 0.311 Chirality : 0.048 0.496 4339 Planarity : 0.004 0.047 4210 Dihedral : 4.492 31.943 3361 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.67 % Favored : 98.23 % Rotamer: Outliers : 2.27 % Allowed : 10.99 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.15), residues: 3115 helix: 2.28 (0.20), residues: 714 sheet: 0.35 (0.19), residues: 680 loop : -0.59 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1149 TYR 0.022 0.001 TYR A 400 PHE 0.016 0.001 PHE C 324 TRP 0.015 0.001 TRP B 201 HIS 0.003 0.001 HIS C 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (24776) covalent geometry : angle 0.56088 / 0.29 (33895) SS BOND : bond 0.00336 / 0.23 ( 45) SS BOND : angle 2.95264 / 1.95 ( 90) hydrogen bonds : bond 0.05610 / 3.81 ( 821) hydrogen bonds : angle 4.31563 / 2.98 ( 2277) link_BETA1-4 : bond 0.00353 / 0.26 ( 33) link_BETA1-4 : angle 1.41715 / 1.08 ( 99) link_NAG-ASN : bond 0.00655 / 0.50 ( 57) link_NAG-ASN : angle 4.12784 / 2.88 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7717.42 seconds wall clock time: 132 minutes 9.51 seconds (7929.51 seconds total)