Starting phenix.real_space_refine on Sat May 24 14:01:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7v_31783/05_2025/7v7v_31783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7v_31783/05_2025/7v7v_31783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7v_31783/05_2025/7v7v_31783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7v_31783/05_2025/7v7v_31783.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7v_31783/05_2025/7v7v_31783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7v_31783/05_2025/7v7v_31783.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.055 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 108 5.16 5 C 16068 2.51 5 N 4117 2.21 5 O 5011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25304 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 16.19, per 1000 atoms: 0.64 Number of scatterers: 25304 At special positions: 0 Unit cell: (139.7, 148.5, 200.2, 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 108 16.00 O 5011 8.00 N 4117 7.00 C 16068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " 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 k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 601 " " NAG C2003 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 280 " " NAG S 1 " - " ASN B 341 " " NAG T 1 " - " ASN B 614 " " NAG U 1 " - " ASN B 707 " " NAG V 1 " - " ASN B 715 " " NAG W 1 " - " ASN B 799 " " NAG X 1 " - " ASN B1072 " " NAG Y 1 " - " ASN B1096 " " NAG Z 1 " - " ASN B1132 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 163 " " NAG c 1 " - " ASN C 232 " " NAG d 1 " - " ASN C 280 " " NAG e 1 " - " ASN C 329 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 7.48 Conformation dependent library (CDL) restraints added in 3.5 seconds 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 46 sheets defined 24.4% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.686A pdb=" N GLU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.324A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.860A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.313A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.670A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.149A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.843A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.112A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.151A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.141A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.677A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.529A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.568A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.937A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.509A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.528A pdb=" N GLN B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.550A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.383A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.767A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.568A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.884A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.462A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 882 Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.306A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.565A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.834A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.756A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.837A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.040A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.238A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.533A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 317 removed outlier: 3.539A pdb=" N THR A 313 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.505A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.181A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.797A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.613A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.544A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.886A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.255A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.316A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 321 through 326 removed outlier: 5.032A pdb=" N ASN B 538 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.369A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.933A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.988A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.057A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.412A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.976A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.045A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.769A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.196A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N VAL C 126 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N GLU C 167 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ILE C 128 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR C 165 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 130 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU C 132 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA C 161 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN C 134 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.100A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.198A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.565A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.513A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1123 removed outlier: 4.552A pdb=" N ALA C1085 " --> pdb=" O SER C1121 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1092 through 1095 1001 hydrogen bonds defined for protein. 2751 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: 10.75 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7983 1.34 - 1.46: 6432 1.46 - 1.58: 11304 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25851 Sorted by residual: bond pdb=" C1 NAG A2002 " pdb=" O5 NAG A2002 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 ... (remaining 25846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 34167 1.58 - 3.15: 903 3.15 - 4.73: 69 4.73 - 6.31: 26 6.31 - 7.89: 11 Bond angle restraints: 35176 Sorted by residual: angle pdb=" C GLU B 482 " pdb=" CA GLU B 482 " pdb=" CB GLU B 482 " ideal model delta sigma weight residual 116.63 110.28 6.35 1.16e+00 7.43e-01 3.00e+01 angle pdb=" N VAL A 157 " pdb=" CA VAL A 157 " pdb=" C VAL A 157 " ideal model delta sigma weight residual 113.39 108.70 4.69 1.47e+00 4.63e-01 1.02e+01 angle pdb=" CA GLU B 482 " pdb=" C GLU B 482 " pdb=" N GLY B 483 " ideal model delta sigma weight residual 119.63 117.05 2.58 8.10e-01 1.52e+00 1.02e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.52 -3.82 1.22e+00 6.72e-01 9.79e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.08 -5.61 2.06e+00 2.36e-01 7.42e+00 ... (remaining 35171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 15484 23.43 - 46.87: 862 46.87 - 70.30: 118 70.30 - 93.74: 29 93.74 - 117.17: 16 Dihedral angle restraints: 16509 sinusoidal: 7519 harmonic: 8990 Sorted by residual: dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual -86.00 -6.10 -79.90 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 -7.14 -78.86 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 16506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4218 0.136 - 0.272: 22 0.272 - 0.409: 0 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 4241 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PRO C 559 " pdb=" N PRO C 559 " pdb=" C PRO C 559 " pdb=" CB PRO C 559 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO A 559 " pdb=" N PRO A 559 " pdb=" C PRO A 559 " pdb=" CB PRO A 559 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 4238 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.032 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 984 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO C 984 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 984 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO C 985 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 985 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 985 " -0.026 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 655 2.70 - 3.25: 24049 3.25 - 3.80: 38256 3.80 - 4.35: 47620 4.35 - 4.90: 82054 Nonbonded interactions: 192634 Sorted by model distance: nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.145 3.040 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.170 3.040 nonbonded pdb=" O ASN A 437 " pdb=" OG SER A 441 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.212 3.040 ... (remaining 192629 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 14 through 1144 or resid 2001 through 2003)) selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 1144 or resid 2001 through 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 1144 or resid 2001 thr \ ough 2003)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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: 3.390 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: 0.030 Extract box with map and model: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 60.570 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 : 0.004 0.080 25975 Z= 0.181 Angle : 0.608 16.060 35508 Z= 0.287 Chirality : 0.047 0.681 4241 Planarity : 0.003 0.048 4446 Dihedral : 14.230 117.173 10601 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 3041 helix: 2.40 (0.22), residues: 668 sheet: 0.82 (0.19), residues: 716 loop : -0.94 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 884 HIS 0.001 0.000 HIS A1062 PHE 0.016 0.001 PHE B 904 TYR 0.016 0.001 TYR B1065 ARG 0.002 0.000 ARG A1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 48) link_NAG-ASN : angle 2.28508 ( 144) link_BETA1-4 : bond 0.00388 ( 36) link_BETA1-4 : angle 1.82263 ( 108) hydrogen bonds : bond 0.11267 ( 1001) hydrogen bonds : angle 5.47611 ( 2751) SS BOND : bond 0.00258 ( 40) SS BOND : angle 1.22045 ( 80) covalent geometry : bond 0.00372 (25851) covalent geometry : angle 0.58199 (35176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7196 (t80) cc_final: 0.6880 (t80) REVERT: A 644 ARG cc_start: 0.7396 (tpp-160) cc_final: 0.7144 (tpm170) REVERT: A 757 PHE cc_start: 0.7975 (p90) cc_final: 0.7160 (p90) REVERT: A 771 GLU cc_start: 0.8243 (tt0) cc_final: 0.7956 (tt0) REVERT: B 52 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 129 LYS cc_start: 0.6971 (mmmm) cc_final: 0.6752 (mttt) REVERT: B 133 PHE cc_start: 0.7998 (m-80) cc_final: 0.7652 (m-80) REVERT: B 140 PHE cc_start: 0.7371 (p90) cc_final: 0.7114 (p90) REVERT: B 240 LEU cc_start: 0.7653 (mm) cc_final: 0.7439 (mp) REVERT: B 243 HIS cc_start: 0.4393 (p-80) cc_final: 0.3916 (p-80) REVERT: B 416 ILE cc_start: 0.8892 (pt) cc_final: 0.8593 (pt) REVERT: B 451 TYR cc_start: 0.7849 (p90) cc_final: 0.6971 (p90) REVERT: B 506 TYR cc_start: 0.8137 (m-80) cc_final: 0.7765 (m-80) REVERT: B 659 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6962 (tm-30) REVERT: B 876 LEU cc_start: 0.8997 (tp) cc_final: 0.8598 (mt) REVERT: B 955 GLN cc_start: 0.8523 (tt0) cc_final: 0.8308 (tt0) REVERT: C 363 TYR cc_start: 0.9060 (m-80) cc_final: 0.8779 (m-80) REVERT: C 572 ASP cc_start: 0.7309 (m-30) cc_final: 0.6847 (m-30) REVERT: C 979 LEU cc_start: 0.9193 (mt) cc_final: 0.8988 (mt) REVERT: C 1140 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8489 (mm-40) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.3657 time to fit residues: 122.1236 Evaluate side-chains 119 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 259 optimal weight: 5.9990 chunk 232 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 240 optimal weight: 30.0000 chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 278 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN B 899 GLN B 976 ASN C 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.141866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083926 restraints weight = 45295.183| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.28 r_work: 0.3007 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 25975 Z= 0.194 Angle : 0.636 10.893 35508 Z= 0.312 Chirality : 0.047 0.280 4241 Planarity : 0.004 0.068 4446 Dihedral : 9.081 111.459 5075 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 0.48 % Allowed : 5.92 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3041 helix: 2.17 (0.21), residues: 686 sheet: 0.80 (0.19), residues: 687 loop : -1.02 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 884 HIS 0.004 0.001 HIS A1046 PHE 0.024 0.002 PHE C 904 TYR 0.024 0.001 TYR A1065 ARG 0.008 0.001 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 48) link_NAG-ASN : angle 1.92089 ( 144) link_BETA1-4 : bond 0.00410 ( 36) link_BETA1-4 : angle 1.77328 ( 108) hydrogen bonds : bond 0.06011 ( 1001) hydrogen bonds : angle 4.96318 ( 2751) SS BOND : bond 0.00476 ( 40) SS BOND : angle 1.62084 ( 80) covalent geometry : bond 0.00473 (25851) covalent geometry : angle 0.61410 (35176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7516 (t80) cc_final: 0.7300 (t80) REVERT: A 235 ARG cc_start: 0.8698 (mtm110) cc_final: 0.8260 (mtm-85) REVERT: A 757 PHE cc_start: 0.8264 (p90) cc_final: 0.8001 (p90) REVERT: A 771 GLU cc_start: 0.8852 (tt0) cc_final: 0.8561 (tt0) REVERT: B 52 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8574 (tm-30) REVERT: B 129 LYS cc_start: 0.7309 (mmmm) cc_final: 0.7054 (mttt) REVERT: B 133 PHE cc_start: 0.7831 (m-80) cc_final: 0.7619 (m-80) REVERT: B 140 PHE cc_start: 0.7540 (p90) cc_final: 0.7282 (p90) REVERT: B 243 HIS cc_start: 0.4408 (p-80) cc_final: 0.3954 (p-80) REVERT: B 451 TYR cc_start: 0.7988 (p90) cc_final: 0.7007 (p90) REVERT: B 506 TYR cc_start: 0.8106 (m-80) cc_final: 0.7739 (m-80) REVERT: C 140 PHE cc_start: 0.7702 (p90) cc_final: 0.7413 (p90) REVERT: C 363 TYR cc_start: 0.9084 (m-80) cc_final: 0.8788 (m-80) REVERT: C 372 PHE cc_start: 0.7958 (m-80) cc_final: 0.7714 (m-80) REVERT: C 572 ASP cc_start: 0.8014 (m-30) cc_final: 0.7708 (m-30) outliers start: 13 outliers final: 10 residues processed: 134 average time/residue: 0.3801 time to fit residues: 81.0533 Evaluate side-chains 118 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 1140 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 19 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 30.0000 chunk 141 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 247 optimal weight: 0.0000 chunk 86 optimal weight: 1.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 GLN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.142456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093337 restraints weight = 47239.907| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.22 r_work: 0.2973 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25975 Z= 0.140 Angle : 0.579 13.540 35508 Z= 0.282 Chirality : 0.045 0.258 4241 Planarity : 0.004 0.050 4446 Dihedral : 8.377 110.793 5075 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 0.67 % Allowed : 9.07 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3041 helix: 2.20 (0.21), residues: 684 sheet: 0.82 (0.19), residues: 683 loop : -1.02 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 884 HIS 0.003 0.001 HIS A1086 PHE 0.017 0.001 PHE C 904 TYR 0.019 0.001 TYR B1065 ARG 0.007 0.000 ARG B 344 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 48) link_NAG-ASN : angle 1.73754 ( 144) link_BETA1-4 : bond 0.00396 ( 36) link_BETA1-4 : angle 1.78827 ( 108) hydrogen bonds : bond 0.05499 ( 1001) hydrogen bonds : angle 4.83255 ( 2751) SS BOND : bond 0.00372 ( 40) SS BOND : angle 1.39841 ( 80) covalent geometry : bond 0.00331 (25851) covalent geometry : angle 0.55877 (35176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8154 (mtm-85) REVERT: A 757 PHE cc_start: 0.8249 (p90) cc_final: 0.7912 (p90) REVERT: B 52 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 140 PHE cc_start: 0.7519 (p90) cc_final: 0.7219 (p90) REVERT: B 243 HIS cc_start: 0.4119 (p-80) cc_final: 0.3671 (p-80) REVERT: B 404 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: B 451 TYR cc_start: 0.7996 (p90) cc_final: 0.7010 (p90) REVERT: B 506 TYR cc_start: 0.8090 (m-80) cc_final: 0.7656 (m-80) REVERT: C 363 TYR cc_start: 0.9100 (m-80) cc_final: 0.8802 (m-80) REVERT: C 372 PHE cc_start: 0.8038 (m-80) cc_final: 0.7780 (m-80) REVERT: C 572 ASP cc_start: 0.7886 (m-30) cc_final: 0.7494 (m-30) outliers start: 18 outliers final: 13 residues processed: 131 average time/residue: 0.3446 time to fit residues: 75.0674 Evaluate side-chains 114 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 2.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 78 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 284 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 chunk 271 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.135193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077462 restraints weight = 46330.976| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.16 r_work: 0.2918 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25975 Z= 0.202 Angle : 0.627 12.432 35508 Z= 0.307 Chirality : 0.047 0.255 4241 Planarity : 0.004 0.052 4446 Dihedral : 8.079 109.104 5075 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.10 % Rotamer: Outliers : 1.55 % Allowed : 10.81 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3041 helix: 2.16 (0.21), residues: 679 sheet: 0.69 (0.19), residues: 689 loop : -1.10 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 884 HIS 0.004 0.001 HIS A1046 PHE 0.023 0.002 PHE B 133 TYR 0.023 0.001 TYR A1065 ARG 0.006 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 48) link_NAG-ASN : angle 1.86409 ( 144) link_BETA1-4 : bond 0.00370 ( 36) link_BETA1-4 : angle 1.81717 ( 108) hydrogen bonds : bond 0.06418 ( 1001) hydrogen bonds : angle 4.95097 ( 2751) SS BOND : bond 0.00435 ( 40) SS BOND : angle 1.51905 ( 80) covalent geometry : bond 0.00496 (25851) covalent geometry : angle 0.60561 (35176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8246 (mtm-85) REVERT: A 757 PHE cc_start: 0.8460 (p90) cc_final: 0.8093 (p90) REVERT: B 52 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8585 (tm-30) REVERT: B 140 PHE cc_start: 0.7477 (p90) cc_final: 0.7028 (p90) REVERT: B 240 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7625 (tp) REVERT: B 404 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: B 506 TYR cc_start: 0.7995 (m-80) cc_final: 0.7763 (m-80) REVERT: B 738 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8744 (tpt) REVERT: C 363 TYR cc_start: 0.9121 (m-80) cc_final: 0.8806 (m-80) REVERT: C 372 PHE cc_start: 0.8073 (m-80) cc_final: 0.7822 (m-80) REVERT: C 572 ASP cc_start: 0.7995 (m-30) cc_final: 0.7690 (m-30) outliers start: 42 outliers final: 19 residues processed: 138 average time/residue: 0.3679 time to fit residues: 85.5013 Evaluate side-chains 117 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 233 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 109 optimal weight: 7.9990 chunk 295 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 chunk 228 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.138814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082630 restraints weight = 46410.828| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.12 r_work: 0.2987 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25975 Z= 0.112 Angle : 0.565 12.199 35508 Z= 0.272 Chirality : 0.044 0.256 4241 Planarity : 0.004 0.049 4446 Dihedral : 7.569 106.187 5075 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.52 % Favored : 96.38 % Rotamer: Outliers : 1.52 % Allowed : 11.62 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3041 helix: 2.31 (0.21), residues: 678 sheet: 0.80 (0.19), residues: 692 loop : -1.03 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 884 HIS 0.002 0.001 HIS B1086 PHE 0.018 0.001 PHE B1119 TYR 0.017 0.001 TYR B1065 ARG 0.003 0.000 ARG B 401 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 48) link_NAG-ASN : angle 1.75475 ( 144) link_BETA1-4 : bond 0.00419 ( 36) link_BETA1-4 : angle 1.84589 ( 108) hydrogen bonds : bond 0.05215 ( 1001) hydrogen bonds : angle 4.75546 ( 2751) SS BOND : bond 0.00313 ( 40) SS BOND : angle 1.18232 ( 80) covalent geometry : bond 0.00249 (25851) covalent geometry : angle 0.54418 (35176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8788 (mtm110) cc_final: 0.8305 (mtm-85) REVERT: A 738 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8706 (tpp) REVERT: A 757 PHE cc_start: 0.8368 (p90) cc_final: 0.7993 (p90) REVERT: B 52 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 140 PHE cc_start: 0.7430 (p90) cc_final: 0.6961 (p90) REVERT: B 404 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: B 451 TYR cc_start: 0.7966 (p90) cc_final: 0.7106 (p90) REVERT: B 506 TYR cc_start: 0.8034 (m-80) cc_final: 0.7747 (m-80) REVERT: C 363 TYR cc_start: 0.9099 (m-80) cc_final: 0.8781 (m-80) REVERT: C 372 PHE cc_start: 0.8073 (m-80) cc_final: 0.7839 (m-80) REVERT: C 558 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9095 (mp) REVERT: C 572 ASP cc_start: 0.8118 (m-30) cc_final: 0.7758 (m-30) REVERT: C 982 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8786 (pt) outliers start: 41 outliers final: 25 residues processed: 146 average time/residue: 0.3286 time to fit residues: 80.7275 Evaluate side-chains 131 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 217 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 147 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 305 optimal weight: 0.0270 chunk 281 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 285 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 20 optimal weight: 7.9990 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.137557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.080195 restraints weight = 46002.665| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.18 r_work: 0.2969 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25975 Z= 0.115 Angle : 0.566 12.372 35508 Z= 0.271 Chirality : 0.044 0.258 4241 Planarity : 0.004 0.049 4446 Dihedral : 7.076 99.788 5075 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 1.55 % Allowed : 12.03 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3041 helix: 2.34 (0.21), residues: 678 sheet: 0.86 (0.19), residues: 684 loop : -1.02 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 884 HIS 0.002 0.000 HIS B1086 PHE 0.017 0.001 PHE B1119 TYR 0.018 0.001 TYR B1065 ARG 0.007 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 48) link_NAG-ASN : angle 1.82215 ( 144) link_BETA1-4 : bond 0.00405 ( 36) link_BETA1-4 : angle 1.84009 ( 108) hydrogen bonds : bond 0.05078 ( 1001) hydrogen bonds : angle 4.69022 ( 2751) SS BOND : bond 0.00322 ( 40) SS BOND : angle 1.12090 ( 80) covalent geometry : bond 0.00262 (25851) covalent geometry : angle 0.54439 (35176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8737 (mtm110) cc_final: 0.8272 (mtm-85) REVERT: A 738 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8637 (tpp) REVERT: A 757 PHE cc_start: 0.8377 (p90) cc_final: 0.8009 (p90) REVERT: B 52 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 133 PHE cc_start: 0.7689 (m-10) cc_final: 0.7136 (m-10) REVERT: B 140 PHE cc_start: 0.7422 (p90) cc_final: 0.6957 (p90) REVERT: B 243 HIS cc_start: 0.4087 (p-80) cc_final: 0.3549 (p-80) REVERT: B 404 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: B 451 TYR cc_start: 0.8025 (p90) cc_final: 0.7242 (p90) REVERT: B 506 TYR cc_start: 0.7986 (m-80) cc_final: 0.7704 (m-80) REVERT: C 363 TYR cc_start: 0.9080 (m-80) cc_final: 0.8761 (m-80) REVERT: C 372 PHE cc_start: 0.8094 (m-80) cc_final: 0.7862 (m-80) REVERT: C 558 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9063 (mp) REVERT: C 572 ASP cc_start: 0.8082 (m-30) cc_final: 0.7670 (m-30) REVERT: C 803 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8889 (mt) REVERT: C 982 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8702 (pt) outliers start: 42 outliers final: 29 residues processed: 144 average time/residue: 0.3191 time to fit residues: 77.5993 Evaluate side-chains 134 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 242 optimal weight: 7.9990 chunk 198 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 91 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 276 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 392 ASN B 976 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.143732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086105 restraints weight = 48763.091| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.18 r_work: 0.2969 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25975 Z= 0.113 Angle : 0.562 12.795 35508 Z= 0.269 Chirality : 0.044 0.258 4241 Planarity : 0.003 0.049 4446 Dihedral : 6.648 90.145 5075 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 1.74 % Allowed : 12.62 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 3041 helix: 2.42 (0.21), residues: 672 sheet: 0.80 (0.19), residues: 702 loop : -1.00 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 884 HIS 0.002 0.000 HIS C 517 PHE 0.018 0.001 PHE A 133 TYR 0.017 0.001 TYR B1065 ARG 0.004 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 48) link_NAG-ASN : angle 1.93095 ( 144) link_BETA1-4 : bond 0.00405 ( 36) link_BETA1-4 : angle 1.81240 ( 108) hydrogen bonds : bond 0.04943 ( 1001) hydrogen bonds : angle 4.64380 ( 2751) SS BOND : bond 0.00311 ( 40) SS BOND : angle 1.03349 ( 80) covalent geometry : bond 0.00256 (25851) covalent geometry : angle 0.53910 (35176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 107 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8681 (mtm110) cc_final: 0.8210 (mtm-85) REVERT: A 738 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8495 (tpp) REVERT: A 757 PHE cc_start: 0.8195 (p90) cc_final: 0.7785 (p90) REVERT: B 52 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8469 (tm-30) REVERT: B 133 PHE cc_start: 0.7777 (m-10) cc_final: 0.7112 (m-10) REVERT: B 140 PHE cc_start: 0.7353 (p90) cc_final: 0.6897 (p90) REVERT: B 243 HIS cc_start: 0.4116 (p-80) cc_final: 0.3591 (p-80) REVERT: B 404 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: B 451 TYR cc_start: 0.7916 (p90) cc_final: 0.7123 (p90) REVERT: B 506 TYR cc_start: 0.7948 (m-80) cc_final: 0.7664 (m-80) REVERT: B 738 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8608 (tpt) REVERT: B 1037 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8640 (mtp180) REVERT: C 363 TYR cc_start: 0.9065 (m-80) cc_final: 0.8734 (m-80) REVERT: C 372 PHE cc_start: 0.8118 (m-80) cc_final: 0.7885 (m-80) REVERT: C 558 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8962 (mp) REVERT: C 572 ASP cc_start: 0.7839 (m-30) cc_final: 0.7388 (m-30) REVERT: C 803 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 982 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8689 (pt) outliers start: 47 outliers final: 31 residues processed: 146 average time/residue: 0.3279 time to fit residues: 80.7411 Evaluate side-chains 141 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 139 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 275 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.142668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084605 restraints weight = 48593.328| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.17 r_work: 0.2939 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25975 Z= 0.146 Angle : 0.584 13.201 35508 Z= 0.280 Chirality : 0.045 0.262 4241 Planarity : 0.004 0.049 4446 Dihedral : 6.572 85.457 5075 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 1.70 % Allowed : 12.77 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3041 helix: 2.30 (0.21), residues: 678 sheet: 0.82 (0.19), residues: 684 loop : -1.04 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 884 HIS 0.003 0.001 HIS A1062 PHE 0.018 0.001 PHE B1119 TYR 0.019 0.001 TYR A1065 ARG 0.004 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 48) link_NAG-ASN : angle 2.03458 ( 144) link_BETA1-4 : bond 0.00376 ( 36) link_BETA1-4 : angle 1.77686 ( 108) hydrogen bonds : bond 0.05454 ( 1001) hydrogen bonds : angle 4.71089 ( 2751) SS BOND : bond 0.00350 ( 40) SS BOND : angle 1.22259 ( 80) covalent geometry : bond 0.00349 (25851) covalent geometry : angle 0.56090 (35176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 100 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7879 (m-80) cc_final: 0.6732 (m-80) REVERT: A 235 ARG cc_start: 0.8687 (mtm110) cc_final: 0.8320 (mtm-85) REVERT: A 738 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8600 (tpp) REVERT: A 757 PHE cc_start: 0.8146 (p90) cc_final: 0.7471 (p90) REVERT: B 52 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 133 PHE cc_start: 0.7802 (m-10) cc_final: 0.7130 (m-10) REVERT: B 140 PHE cc_start: 0.7375 (p90) cc_final: 0.6928 (p90) REVERT: B 404 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: B 451 TYR cc_start: 0.7988 (p90) cc_final: 0.7195 (p90) REVERT: B 738 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8664 (tpt) REVERT: B 1037 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8612 (mtp180) REVERT: C 363 TYR cc_start: 0.9081 (m-80) cc_final: 0.8788 (m-80) REVERT: C 372 PHE cc_start: 0.8152 (m-80) cc_final: 0.7931 (m-80) REVERT: C 572 ASP cc_start: 0.7873 (m-30) cc_final: 0.7452 (m-30) REVERT: C 803 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8867 (mt) REVERT: C 982 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8720 (pt) outliers start: 46 outliers final: 37 residues processed: 138 average time/residue: 0.3406 time to fit residues: 79.5453 Evaluate side-chains 142 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 96 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 243 optimal weight: 0.0470 chunk 137 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.135155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.078009 restraints weight = 46456.787| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.51 r_work: 0.2893 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25975 Z= 0.188 Angle : 0.622 13.250 35508 Z= 0.301 Chirality : 0.046 0.264 4241 Planarity : 0.004 0.050 4446 Dihedral : 6.624 82.370 5075 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 1.85 % Allowed : 12.77 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3041 helix: 2.19 (0.21), residues: 681 sheet: 0.66 (0.20), residues: 667 loop : -1.12 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 884 HIS 0.003 0.001 HIS B1046 PHE 0.020 0.001 PHE B1119 TYR 0.021 0.001 TYR A1065 ARG 0.006 0.000 ARG B1037 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 48) link_NAG-ASN : angle 2.17261 ( 144) link_BETA1-4 : bond 0.00361 ( 36) link_BETA1-4 : angle 1.77625 ( 108) hydrogen bonds : bond 0.06265 ( 1001) hydrogen bonds : angle 4.86288 ( 2751) SS BOND : bond 0.00428 ( 40) SS BOND : angle 1.47045 ( 80) covalent geometry : bond 0.00460 (25851) covalent geometry : angle 0.59711 (35176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7955 (m-80) cc_final: 0.6862 (m-80) REVERT: A 235 ARG cc_start: 0.8674 (mtm110) cc_final: 0.8313 (mtm-85) REVERT: A 757 PHE cc_start: 0.8146 (p90) cc_final: 0.7523 (p90) REVERT: B 52 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8464 (tm-30) REVERT: B 133 PHE cc_start: 0.7964 (m-10) cc_final: 0.7273 (m-10) REVERT: B 140 PHE cc_start: 0.7461 (p90) cc_final: 0.6902 (p90) REVERT: B 240 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7635 (tt) REVERT: B 738 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8796 (tpt) REVERT: B 1037 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8580 (mtp180) REVERT: C 363 TYR cc_start: 0.9113 (m-80) cc_final: 0.8845 (m-80) REVERT: C 372 PHE cc_start: 0.8144 (m-80) cc_final: 0.7942 (m-80) REVERT: C 459 LEU cc_start: 0.3869 (OUTLIER) cc_final: 0.3317 (tp) REVERT: C 572 ASP cc_start: 0.7830 (m-30) cc_final: 0.7398 (m-30) REVERT: C 803 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8858 (mt) REVERT: C 982 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8717 (pt) outliers start: 50 outliers final: 37 residues processed: 142 average time/residue: 0.3503 time to fit residues: 82.3812 Evaluate side-chains 140 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 30.0000 chunk 6 optimal weight: 3.9990 chunk 194 optimal weight: 0.0470 chunk 24 optimal weight: 2.9990 chunk 142 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 252 optimal weight: 0.0670 chunk 221 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 overall best weight: 0.8358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.136876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.079360 restraints weight = 46074.888| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.17 r_work: 0.2954 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25975 Z= 0.118 Angle : 0.575 13.097 35508 Z= 0.277 Chirality : 0.044 0.262 4241 Planarity : 0.004 0.049 4446 Dihedral : 6.417 81.438 5075 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.88 % Favored : 96.02 % Rotamer: Outliers : 1.63 % Allowed : 13.21 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3041 helix: 2.28 (0.21), residues: 678 sheet: 0.78 (0.19), residues: 694 loop : -1.03 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 884 HIS 0.002 0.000 HIS B1086 PHE 0.019 0.001 PHE B1119 TYR 0.018 0.001 TYR C 493 ARG 0.007 0.000 ARG B 344 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 48) link_NAG-ASN : angle 2.10064 ( 144) link_BETA1-4 : bond 0.00394 ( 36) link_BETA1-4 : angle 1.76763 ( 108) hydrogen bonds : bond 0.05315 ( 1001) hydrogen bonds : angle 4.71587 ( 2751) SS BOND : bond 0.00321 ( 40) SS BOND : angle 1.14200 ( 80) covalent geometry : bond 0.00269 (25851) covalent geometry : angle 0.55106 (35176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7954 (m-80) cc_final: 0.6836 (m-80) REVERT: A 168 TYR cc_start: 0.7376 (t80) cc_final: 0.7062 (t80) REVERT: A 235 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8412 (mtm-85) REVERT: A 738 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8729 (tpp) REVERT: B 52 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8535 (tm-30) REVERT: B 133 PHE cc_start: 0.7981 (m-10) cc_final: 0.7294 (m-10) REVERT: B 140 PHE cc_start: 0.7409 (p90) cc_final: 0.6868 (p90) REVERT: B 240 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7628 (tt) REVERT: B 344 ARG cc_start: 0.7481 (ttp80) cc_final: 0.7234 (ttp80) REVERT: B 404 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: B 1037 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8675 (mtp180) REVERT: C 363 TYR cc_start: 0.9086 (m-80) cc_final: 0.8807 (m-80) REVERT: C 459 LEU cc_start: 0.3855 (OUTLIER) cc_final: 0.3265 (tp) REVERT: C 572 ASP cc_start: 0.8049 (m-30) cc_final: 0.7610 (m-30) REVERT: C 803 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8886 (mt) REVERT: C 982 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8685 (pt) outliers start: 44 outliers final: 37 residues processed: 144 average time/residue: 0.3284 time to fit residues: 79.7966 Evaluate side-chains 145 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6527 > 50: distance: 84 - 139: 27.804 distance: 87 - 136: 31.323 distance: 123 - 128: 29.631 distance: 128 - 129: 24.428 distance: 129 - 130: 23.689 distance: 129 - 132: 20.298 distance: 130 - 131: 15.827 distance: 130 - 136: 48.804 distance: 132 - 133: 37.835 distance: 133 - 134: 21.993 distance: 133 - 135: 19.769 distance: 136 - 137: 49.825 distance: 137 - 138: 27.561 distance: 137 - 140: 35.691 distance: 138 - 139: 20.520 distance: 138 - 145: 28.460 distance: 140 - 141: 44.728 distance: 141 - 142: 30.618 distance: 142 - 143: 24.455 distance: 142 - 144: 23.246 distance: 145 - 146: 16.142 distance: 146 - 147: 17.524 distance: 146 - 149: 48.430 distance: 147 - 148: 17.281 distance: 147 - 151: 21.102 distance: 149 - 150: 16.507 distance: 151 - 152: 9.645 distance: 152 - 153: 10.002 distance: 152 - 155: 41.090 distance: 153 - 154: 37.177 distance: 153 - 163: 41.165 distance: 155 - 156: 27.053 distance: 156 - 157: 15.251 distance: 156 - 158: 37.777 distance: 157 - 159: 41.408 distance: 158 - 160: 40.637 distance: 159 - 161: 19.142 distance: 160 - 161: 14.224 distance: 161 - 162: 19.149 distance: 163 - 164: 39.411 distance: 164 - 165: 39.545 distance: 165 - 167: 21.410 distance: 167 - 168: 30.781 distance: 168 - 169: 23.742 distance: 168 - 171: 27.874 distance: 169 - 178: 7.954 distance: 171 - 172: 3.286 distance: 172 - 173: 55.385 distance: 172 - 174: 9.361 distance: 173 - 175: 33.132 distance: 174 - 176: 11.848 distance: 175 - 177: 7.160 distance: 176 - 177: 42.118 distance: 178 - 179: 39.347 distance: 179 - 180: 28.631 distance: 179 - 182: 44.650 distance: 180 - 181: 48.525 distance: 180 - 187: 44.064 distance: 182 - 183: 21.027 distance: 183 - 184: 10.154 distance: 184 - 185: 43.159 distance: 184 - 186: 33.988 distance: 187 - 188: 48.531 distance: 187 - 193: 34.011 distance: 188 - 189: 34.510 distance: 188 - 191: 12.574 distance: 189 - 190: 14.590 distance: 189 - 194: 31.617 distance: 191 - 192: 13.987 distance: 192 - 193: 14.201 distance: 194 - 195: 32.433 distance: 195 - 196: 67.653 distance: 195 - 198: 51.256 distance: 196 - 197: 14.547 distance: 196 - 201: 16.367 distance: 198 - 199: 17.038 distance: 198 - 200: 39.629 distance: 201 - 202: 14.178 distance: 202 - 203: 16.230 distance: 202 - 205: 32.698 distance: 203 - 204: 33.660 distance: 203 - 209: 32.533 distance: 205 - 206: 25.272 distance: 206 - 207: 31.047 distance: 206 - 208: 36.914