Starting phenix.real_space_refine on Fri Jun 13 15:46:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vl5_21230/06_2025/6vl5_21230.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vl5_21230/06_2025/6vl5_21230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vl5_21230/06_2025/6vl5_21230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vl5_21230/06_2025/6vl5_21230.map" model { file = "/net/cci-nas-00/data/ceres_data/6vl5_21230/06_2025/6vl5_21230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vl5_21230/06_2025/6vl5_21230.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 99 5.16 5 C 9378 2.51 5 N 2478 2.21 5 O 3084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15039 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "D" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "B" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "E" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3536 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 20, 'TRANS': 427} Chain breaks: 3 Chain: "F" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 996 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} 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: "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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" 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 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 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 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" 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: 10.18, per 1000 atoms: 0.68 Number of scatterers: 15039 At special positions: 0 Unit cell: (126.5, 127.65, 117.3, 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 99 16.00 O 3084 8.00 N 2478 7.00 C 9378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.07 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.07 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.07 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.10 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA Q 3 " - " MAN Q 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA Q 3 " - " MAN Q 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 Q 2 " - " BMA Q 3 " " 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 a 2 " - " BMA a 3 " " 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-ASN " NAG A 608 " - " ASN A 160 " " NAG A 609 " - " ASN A 276 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 363 " " NAG A 618 " - " ASN A 133 " " NAG A 627 " - " ASN A 289 " " NAG A 630 " - " ASN A 339 " " NAG A 631 " - " ASN A 355 " " NAG A 632 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 608 " - " ASN C 160 " " NAG C 609 " - " ASN C 276 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 363 " " NAG C 618 " - " ASN C 133 " " NAG C 627 " - " ASN C 289 " " NAG C 630 " - " ASN C 339 " " NAG C 631 " - " ASN C 355 " " NAG C 632 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 608 " - " ASN E 160 " " NAG E 609 " - " ASN E 276 " " NAG E 612 " - " ASN E 386 " " NAG E 613 " - " ASN E 363 " " NAG E 618 " - " ASN E 133 " " NAG E 627 " - " ASN E 289 " " NAG E 630 " - " ASN E 339 " " NAG E 631 " - " ASN E 355 " " NAG E 632 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG H 1 " - " ASN C 448 " " NAG I 1 " - " ASN C 295 " " NAG J 1 " - " ASN C 234 " " NAG K 1 " - " ASN C 197 " " NAG L 1 " - " ASN C 156 " " NAG M 1 " - " ASN C 301 " " NAG N 1 " - " ASN C 88 " " NAG O 1 " - " ASN C 241 " " NAG P 1 " - " ASN C 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 234 " " NAG U 1 " - " ASN A 197 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 301 " " NAG X 1 " - " ASN A 88 " " NAG Y 1 " - " ASN A 241 " " NAG Z 1 " - " ASN A 332 " " NAG a 1 " - " ASN E 262 " " NAG b 1 " - " ASN E 448 " " NAG c 1 " - " ASN E 295 " " NAG d 1 " - " ASN E 234 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 156 " " NAG g 1 " - " ASN E 301 " " NAG h 1 " - " ASN E 88 " " NAG i 1 " - " ASN E 241 " " NAG j 1 " - " ASN E 332 " Time building additional restraints: 5.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3216 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 29.1% alpha, 52.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.519A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 535 removed outlier: 3.537A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 Processing helix chain 'D' and resid 543 through 544 No H-bonds generated for 'chain 'D' and resid 543 through 544' Processing helix chain 'D' and resid 545 through 549 Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG D 579 " --> pdb=" O GLN D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.518A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 3.537A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 543 through 544 No H-bonds generated for 'chain 'B' and resid 543 through 544' Processing helix chain 'B' and resid 545 through 549 Processing helix chain 'B' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.893A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.520A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 removed outlier: 3.536A pdb=" N MET F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 543 through 544 No H-bonds generated for 'chain 'F' and resid 543 through 544' Processing helix chain 'F' and resid 545 through 549 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.733A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.406A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 removed outlier: 3.840A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.479A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 4.045A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 316 through 323A removed outlier: 5.491A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.934A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 394 through 396 removed outlier: 6.377A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.405A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.841A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.046A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 316 through 323A removed outlier: 5.492A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.933A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 394 through 396 removed outlier: 6.377A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.404A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 56 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.840A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.480A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.546A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 271 through 273 removed outlier: 4.046A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.492A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.933A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 10.879A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.982A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.825A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 394 through 396 removed outlier: 6.378A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1827 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: 6.02 Time building geometry restraints manager: 6.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3278 1.32 - 1.45: 4445 1.45 - 1.58: 7459 1.58 - 1.71: 4 1.71 - 1.84: 129 Bond restraints: 15315 Sorted by residual: bond pdb=" NE ARG E 308 " pdb=" CZ ARG E 308 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.27e+01 bond pdb=" CZ ARG C 503 " pdb=" NH2 ARG C 503 " ideal model delta sigma weight residual 1.330 1.284 0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" NE ARG A 308 " pdb=" CZ ARG A 308 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.24e+01 bond pdb=" CA ASN C 279 " pdb=" CB ASN C 279 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.27e-02 6.20e+03 1.24e+01 bond pdb=" CB HIS C 85 " pdb=" CG HIS C 85 " ideal model delta sigma weight residual 1.497 1.448 0.049 1.40e-02 5.10e+03 1.24e+01 ... (remaining 15310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 15250 1.67 - 3.33: 4231 3.33 - 5.00: 970 5.00 - 6.67: 284 6.67 - 8.34: 58 Bond angle restraints: 20793 Sorted by residual: angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.10 -8.23 1.04e+00 9.25e-01 6.26e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.87 128.04 -8.17 1.04e+00 9.25e-01 6.17e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.04 -8.17 1.04e+00 9.25e-01 6.17e+01 angle pdb=" N ILE A 213 " pdb=" CA ILE A 213 " pdb=" C ILE A 213 " ideal model delta sigma weight residual 107.84 99.50 8.34 1.11e+00 8.12e-01 5.64e+01 angle pdb=" N ILE E 213 " pdb=" CA ILE E 213 " pdb=" C ILE E 213 " ideal model delta sigma weight residual 107.84 99.53 8.31 1.11e+00 8.12e-01 5.61e+01 ... (remaining 20788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 10086 21.55 - 43.11: 342 43.11 - 64.66: 90 64.66 - 86.21: 21 86.21 - 107.77: 15 Dihedral angle restraints: 10554 sinusoidal: 5589 harmonic: 4965 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.83 42.83 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.82 42.82 1 1.00e+01 1.00e-02 2.56e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.80 42.80 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 10551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1927 0.111 - 0.223: 651 0.223 - 0.334: 65 0.334 - 0.445: 12 0.445 - 0.557: 3 Chirality restraints: 2658 Sorted by residual: chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.00e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.88e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.65e+01 ... (remaining 2655 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " -0.078 2.00e-02 2.50e+03 8.08e-02 8.16e+01 pdb=" CG ASN A 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG A 630 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " -0.078 2.00e-02 2.50e+03 8.07e-02 8.15e+01 pdb=" CG ASN C 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG C 630 " -0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " -0.078 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" CG ASN E 339 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " 0.126 2.00e-02 2.50e+03 pdb=" C1 NAG E 630 " -0.096 2.00e-02 2.50e+03 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3191 2.77 - 3.31: 13968 3.31 - 3.84: 25723 3.84 - 4.37: 30643 4.37 - 4.90: 48262 Nonbonded interactions: 121787 Sorted by model distance: nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.243 3.040 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.367 3.120 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP B 632 " model vdw 2.368 3.120 ... (remaining 121782 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' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = 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 '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 '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' } Set up NCS constraints Number of NCS constrained groups: 4 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } pdb_interpretation.ncs_group { reference = 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 '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 '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' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 40.350 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.019 0.090 15453 Z= 1.006 Angle : 1.751 9.210 21174 Z= 1.093 Chirality : 0.104 0.557 2658 Planarity : 0.009 0.043 2499 Dihedral : 11.989 107.765 7239 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 0.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.20 % Allowed : 1.57 % Favored : 98.24 % 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: 0.88 (0.19), residues: 1683 helix: 0.15 (0.24), residues: 426 sheet: 1.08 (0.23), residues: 405 loop : 0.76 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.011 TRP A 479 HIS 0.010 0.002 HIS E 85 PHE 0.031 0.006 PHE E 383 TYR 0.040 0.007 TYR E 319 ARG 0.010 0.001 ARG C 298 Details of bonding type rmsd link_NAG-ASN : bond 0.02920 ( 66) link_NAG-ASN : angle 2.56024 ( 198) link_ALPHA1-6 : bond 0.03389 ( 3) link_ALPHA1-6 : angle 2.62673 ( 9) link_BETA1-4 : bond 0.03792 ( 33) link_BETA1-4 : angle 3.68898 ( 99) link_ALPHA1-3 : bond 0.03995 ( 3) link_ALPHA1-3 : angle 3.17604 ( 9) hydrogen bonds : bond 0.15492 ( 555) hydrogen bonds : angle 7.37052 ( 1827) SS BOND : bond 0.02664 ( 33) SS BOND : angle 1.88030 ( 66) covalent geometry : bond 0.01884 (15315) covalent geometry : angle 1.72480 (20793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8423 (m-80) cc_final: 0.7822 (m-80) REVERT: A 40 TYR cc_start: 0.8768 (t80) cc_final: 0.7534 (p90) REVERT: A 49 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7492 (mm-30) REVERT: A 50 THR cc_start: 0.9322 (t) cc_final: 0.9081 (t) REVERT: A 63 THR cc_start: 0.6150 (p) cc_final: 0.5866 (p) REVERT: A 108 ILE cc_start: 0.9560 (mt) cc_final: 0.9270 (mt) REVERT: A 116 LEU cc_start: 0.9484 (tp) cc_final: 0.9272 (pp) REVERT: A 175 LEU cc_start: 0.8934 (mt) cc_final: 0.8461 (pt) REVERT: A 319 TYR cc_start: 0.8416 (p90) cc_final: 0.7944 (p90) REVERT: A 384 TYR cc_start: 0.9200 (m-80) cc_final: 0.8684 (m-80) REVERT: A 483 LEU cc_start: 0.9290 (mt) cc_final: 0.8952 (pp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1478 time to fit residues: 21.2604 Evaluate side-chains 58 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.432 Evaluate side-chains 70 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 540 GLN cc_start: 0.7994 (mm110) cc_final: 0.7779 (mt0) REVERT: B 544 LEU cc_start: 0.9276 (mm) cc_final: 0.8809 (mm) REVERT: B 545 LEU cc_start: 0.8971 (mt) cc_final: 0.8497 (pt) REVERT: B 575 GLN cc_start: 0.8881 (mt0) cc_final: 0.8365 (mp10) REVERT: B 576 LEU cc_start: 0.9072 (tp) cc_final: 0.8810 (tt) REVERT: B 579 ARG cc_start: 0.8577 (mtp180) cc_final: 0.7551 (ptt180) REVERT: B 610 TRP cc_start: 0.6697 (t-100) cc_final: 0.6099 (p90) REVERT: B 635 ILE cc_start: 0.9183 (pt) cc_final: 0.8874 (pt) REVERT: B 646 LEU cc_start: 0.9740 (mt) cc_final: 0.9493 (mm) REVERT: B 649 SER cc_start: 0.9433 (m) cc_final: 0.8641 (m) REVERT: B 650 GLN cc_start: 0.8766 (tp40) cc_final: 0.8135 (tm-30) REVERT: B 652 GLN cc_start: 0.8914 (mt0) cc_final: 0.8625 (mm-40) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1438 time to fit residues: 10.8501 Evaluate side-chains 39 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.128 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0042 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0023 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 50 optimal weight: 0.1980 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061188 restraints weight = 14046.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.063260 restraints weight = 8088.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064750 restraints weight = 5372.313| |-----------------------------------------------------------------------------| r_work (final): 0.3043 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.080016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.065907 restraints weight = 4498.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.067704 restraints weight = 2590.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068907 restraints weight = 1738.067| |-----------------------------------------------------------------------------| r_work (final): 0.3120 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.056597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.050703 restraints weight = 290.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.051737 restraints weight = 101.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051800 restraints weight = 63.608| |-----------------------------------------------------------------------------| r_work (final): 0.2697 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2227 r_free = 0.2227 target = 0.037184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.036921 restraints weight = 147.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2227 r_free = 0.2227 target = 0.037065 restraints weight = 14.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2227 r_free = 0.2227 target = 0.037153 restraints weight = 2.873 | |-----------------------------------------------------------------------------| r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 15453 Z= 0.364 Angle : 1.297 30.960 21174 Z= 0.623 Chirality : 0.059 0.313 2658 Planarity : 0.009 0.193 2499 Dihedral : 10.105 90.330 4005 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.59 % Allowed : 3.91 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 0.07 (0.19), residues: 1683 helix: 0.14 (0.24), residues: 408 sheet: 0.57 (0.22), residues: 465 loop : -0.19 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.005 TRP C 96 HIS 0.016 0.004 HIS E 66 PHE 0.024 0.004 PHE A 383 TYR 0.025 0.004 TYR C 39 ARG 0.009 0.001 ARG B 588 Details of bonding type rmsd link_NAG-ASN : bond 0.01123 ( 66) link_NAG-ASN : angle 7.18512 ( 198) link_ALPHA1-6 : bond 0.00796 ( 3) link_ALPHA1-6 : angle 2.03982 ( 9) link_BETA1-4 : bond 0.00840 ( 33) link_BETA1-4 : angle 1.93704 ( 99) link_ALPHA1-3 : bond 0.02054 ( 3) link_ALPHA1-3 : angle 1.66902 ( 9) hydrogen bonds : bond 0.09374 ( 555) hydrogen bonds : angle 6.02316 ( 1827) SS BOND : bond 0.01382 ( 33) SS BOND : angle 3.74059 ( 66) covalent geometry : bond 0.00826 (15315) covalent geometry : angle 1.07574 (20793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.395 Fit side-chains REVERT: E 86 LEU cc_start: 0.9072 (mm) cc_final: 0.8710 (mm) REVERT: E 96 TRP cc_start: 0.8629 (m-90) cc_final: 0.8334 (m-10) REVERT: E 104 MET cc_start: 0.8823 (mmm) cc_final: 0.8547 (tpp) REVERT: E 127 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8147 (p) REVERT: E 308 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7818 (ttt180) REVERT: E 483 LEU cc_start: 0.9126 (mt) cc_final: 0.8630 (mt) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.1638 time to fit residues: 14.6031 Evaluate side-chains 57 residues out of total 403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.413 Evaluate side-chains 52 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 540 GLN cc_start: 0.8218 (mm110) cc_final: 0.8018 (mt0) REVERT: F 575 GLN cc_start: 0.8488 (mt0) cc_final: 0.8209 (mt0) REVERT: F 579 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7362 (ptt180) REVERT: F 628 TRP cc_start: 0.7296 (m-10) cc_final: 0.5461 (p-90) REVERT: F 649 SER cc_start: 0.9214 (m) cc_final: 0.8314 (m) REVERT: F 651 ASN cc_start: 0.9099 (t0) cc_final: 0.8833 (t0) REVERT: F 652 GLN cc_start: 0.9119 (mt0) cc_final: 0.8857 (mm-40) outliers start: 1 outliers final: 0 residues processed: 51 average time/residue: 0.1344 time to fit residues: 7.5002 Evaluate side-chains 34 residues out of total 108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.109 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0037 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0021 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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: 60.7178 > 50: distance: 1 - 2: 4.966 distance: 2 - 3: 9.697 distance: 2 - 9: 8.207 distance: 4 - 5: 3.852 distance: 6 - 7: 3.399 distance: 6 - 8: 4.498 distance: 9 - 10: 9.231 distance: 10 - 11: 20.926 distance: 10 - 13: 14.374 distance: 11 - 12: 49.593 distance: 11 - 20: 17.047 distance: 13 - 14: 8.031 distance: 14 - 15: 5.635 distance: 14 - 16: 9.636 distance: 15 - 17: 7.191 distance: 16 - 18: 9.199 distance: 17 - 19: 20.869 distance: 18 - 19: 14.899 distance: 20 - 21: 23.443 distance: 21 - 22: 28.018 distance: 21 - 24: 10.296 distance: 22 - 23: 29.256 distance: 22 - 28: 18.913 distance: 24 - 25: 32.194 distance: 25 - 26: 14.541 distance: 25 - 27: 18.265 distance: 28 - 29: 26.371 distance: 29 - 30: 21.948 distance: 29 - 32: 21.101 distance: 30 - 31: 21.851 distance: 30 - 36: 4.011 distance: 32 - 33: 26.568 distance: 33 - 34: 32.819 distance: 34 - 35: 22.554 distance: 36 - 37: 19.321 distance: 37 - 38: 7.041 distance: 37 - 40: 17.039 distance: 38 - 39: 24.608 distance: 38 - 50: 22.164 distance: 40 - 41: 17.087 distance: 41 - 42: 9.104 distance: 41 - 43: 19.071 distance: 42 - 44: 15.151 distance: 43 - 45: 25.592 distance: 43 - 46: 13.079 distance: 44 - 45: 27.805 distance: 45 - 47: 28.709 distance: 46 - 48: 11.334 distance: 47 - 49: 18.943 distance: 48 - 49: 11.150 distance: 50 - 51: 25.963 distance: 51 - 52: 19.946 distance: 51 - 54: 37.356 distance: 52 - 53: 39.804 distance: 52 - 59: 24.233 distance: 54 - 55: 53.729 distance: 55 - 56: 31.829 distance: 56 - 57: 7.043 distance: 57 - 58: 6.580 distance: 59 - 60: 19.720 distance: 60 - 61: 47.708 distance: 60 - 63: 21.945 distance: 61 - 62: 36.450 distance: 61 - 67: 44.017 distance: 63 - 64: 12.054 distance: 64 - 65: 12.758 distance: 64 - 66: 13.937 distance: 67 - 68: 11.003 distance: 68 - 69: 23.385 distance: 68 - 71: 20.629 distance: 69 - 70: 57.223 distance: 69 - 75: 17.955 distance: 71 - 72: 8.562 distance: 72 - 74: 4.180 distance: 75 - 76: 14.736 distance: 76 - 77: 12.521 distance: 76 - 79: 22.883 distance: 77 - 78: 33.445 distance: 77 - 83: 12.801 distance: 79 - 80: 19.137 distance: 80 - 81: 37.324 distance: 81 - 82: 20.398 distance: 83 - 84: 8.220 distance: 84 - 85: 4.761 distance: 84 - 87: 13.230 distance: 85 - 86: 7.923 distance: 87 - 88: 6.608 distance: 87 - 89: 8.602